I don’t have “Show Calendars from iOS” checked. Adding directly to Fantastical works well and you still have the choice whether to enable a directly added account on a device. E.g., I sign in with my work calendar on personal devices but I don’t sign in with personal on my work devices (they appear in Settings > Accounts as greyed out options I can enable on the work computer.) So I’m not giving up any kind of flexibility by using direct adding.
I don’t have it selected, and use the Flexibits sync. Zero problems with this setup. I do not have them set up with the default calendar at all as I don’t need it.
I am actually the other way around. I cannot use fantastical for my work calendars. however, I can use fantastical on my work devices as a subscriber and see my personal calendar there. This is handy when booking meeting to check if there is something on the personal calendar that may conflict.
I suppose, I could have added my personal calendar to my work iPhone directly but I didn’t feel comfortable doing that. Now, I am thinking, perhaps, there is no different using fantastical to access personal calendars on work devices as opposed to adding personal calendars on the calendar app on work devices.