Well your 2018 Mini will come nuked and paved for you, so the first part is done 
. Putting the data back where it belongs is always the easy part of that process – the hard part is getting apps, scripts, preferences etc. in place but it sounds like your plan is to put these on the built-in drive anyway… Can CCC or Migration Assistant (long time since I’ve used either…) just restore everything but your data directories? Presumably you’re going to be symlinking directories off the Mini to the external SSD right? I’d just boot up the 2018 Mini, set up the symlinks, then restore the data from a backup, relying on the symlinks to move stuff to the external drive where necessary.
Here are my notes on a similar process - the whole thread may be helpful: