Based on this, it would seem that my system is about as “future proof” as one can get provided I do my linking in Obsidian rather than DT, correct?
True. I only meant that there are many formats suitable for archiving data.
That is a great resource. Having adopted a system (see above) for dealing with my research files that end up in both Obsidian and DT and that are linked from within Obsidian, I used DEVONthink’s web clipper to add that webpage to DT. It showed up as it should in the Finder and my Obsidian vault with only one click. For the automation gurus on this site this is small stuff but for me it brings satisfaction. My system is working extremely well and I have all of my written notes in markdown by exporting them from Apple Notes with the Exporter app. 
DT Clipper
DT Database
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Finder
Obsidian
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If you put the actual folders/files in DevonThink as opposed to indexing, would they still link the same way? If not, and if DT is just using the functionality of Obsidian to maintain the links, I don’t understand how indexing in DT has any effect on future-proofing?
Yes, but you’d lose the folder structure that Obsidian creates. And Obsidian wouldn’t be able to work with them. You don’t want other software messing with items directly in DT’s database folders.
Which means you’re correct - indexing with DT doesn’t have an effect on future-proofing. But it might increase present usability, depending on the use case. 
As long as you mean that Obsidian is your Source Of Truth, yes - that would be my take on it.
Well, it is “a” source of truth but not “THE” source of truth.
Seriously, all of my research files are in an iCloud folder, indexed in DT and accessed in an Obsidian Vault. Also, I maintain three separate backups. All linking is with Obsidian, so I’m probably about as good as can be done.
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I think I’m wired a lot like you are. I hugely regret spending money on Nick Milo’s courses, but I know other people Think they were life changing.
Which plugin? I went to click through and found nothing. I was intrigued 
I do use obsidian but just as note taking and journaling tool. It is a pain ton
Sorry, looks like Discourse ate the Obsidian deep link. Here’s the GitHub repo.
The key is since Obsidian uses markdown, that “someone” doesn’t have to be the developer, or a random person on the Internet. That someone can be me in 10 minutes with a Python script.
In any case, I haven’t really found anything that does linking that doesn’t cost me an arm and a leg and that has Vim support. If you know of one I’d love to hear it about it though, would be open to switching.
W.r.t. future proofing of inter-note links, I personally think that it’s most important to include the note’s ID (i.e., the URL/path/string/etc that’s used for linking) within the note body itself. Notes should be self-contained.
That way, you won’t depend on the app that created the links since you can always search for the link ID which would return the note with that ID plus all notes linking to it. And, if necessary, someone could then write a script to transform the links into another format.
Including the link ID within the note itself also helps with path-based link systems like Obsidian, where externally renaming or moving a file could break the link.
Btw, this topic was also discussed in the DEVONthink forums:
Fair enough, although if you’re using Obsidian to do your renaming and such it cleans up all your notes natively. You would, as you say, have to be operating on your Obsidian data using another piece of software in order to introduce corruption in the link scheme.
I was on another forum where someone mentioned this as well, and Nick himself got involved in the discussion. I believe it was on Reddit.
I don’t mean to start a war here, if his courses or advice have helped you that’s great, but I have to get this off my chest. Does no one find him to be a little disingenuous? He’s so soft spoken in his videos but the whole vibe comes across like he’s yelling at someone behind the scenes in between takes and there’s so much tension in the room. Seeing his responses to some online criticism only makes me feel this way even more.
Like I said, if you find his teachings valuable (and many do) good on you and good on him. He obviously knows his stuff. For me personally, I can’t shake the vibe that he’s got a bit of a temper and is in this for the cash and the notoriety more than the love of the game, but again – not for me to judge. It’s just like, my opinion, man.
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So if you could replicate the linking functionality of Obsidian in 10 minutes, then what’s the point of Obsidian? If your answer is that it includes so much more functionality, then maybe a 10 minute script doesn’t really restore full functionality?
Convenience and a smoother workflow. And a mobile app. And it looks nice, and I don’t need to maintain it myself. Like I’ve said above, Obsidian is no magic software to me. But that’s what makes it great: no nonsense, just gets the job done.
No doubt Obsidian has a lot more powerful linking features I can’t replicate but I don’t use them so they’re irrelevant to me.
I appreciate your distinction between future-proofing of data versus the future-proofing of function. It’s a distinction I don’t think is often made. I can agree that future-proofing is “better” for data when the data you can export from an app is identical to the data you entered into an app.
However, I don’t agree that the data exported from Obsidian is somehow “better future-proofing” because it includes non-functional brackets around words or phrases that the user included in a text file, or because DevonThink puts data into a proprietary database. In both apps you’re still simply getting out what you put in, divorced from the functionality provided by an app.
In DevonThink, in the same way as with Obsidian, what you get out is exactly what you put in. If I put in a photo, a movie, an audio file, a rich text file, a MindNode mind map, or even a markdown file with brackets around words, that’s what I get back.
So there is no “better” here in regard to future-proofing of data. You have the same result from both apps; what you get out is what you put in.
On the other hand, some apps take the data you input and convert it into a proprietary format, and you don’t get out the same format you put in. In comparison to those kinds of apps, I would agree that in apps like Obsidian and DevonThink the “future-proofing is definitely better.”
So you agree you couldn’t actually replicate the functionality of Obsidian with a 10 minute script.
I didn’t mean replicate as an exact clone. Functionally, the links would still work with said script. But, rather obviously, it would not be ideal, given the sheer number of hours that the Obsidian devs have poured into the app.
However, it’s still more convenient than replicating functionality for any other app I’ve found. Once again, I’m open to being shown apps that you or anyone else on this forum thinks meets the criteria above.
*Also note that I did not say I could replicate the entirety of Obsidian either: I am specifically talking about the linking functionality that I use, which is the rather simple double bracket syntax as well as the block-level linking syntax.
I imagine it all comes down to what kind of functionality you personally value. For my workflow and needs, I don’t see great value in Obsidian. I get my functionality of choice from other apps.
You’ll have to direct your question to those who value that same functionality that you do.