I've been playing around with this for an hour or so this morning and the move to separate folders has honestly broken a lot in terms of the includes.
I've been working with /admin as an example. Even if we set the base working directory to fix the relative file paths (chdir(__DIR__ . '/..');), we still get the issue of CSS/JS resources not linking correctly unless we set <base href='admin'/> but that should only appear in the page header.
The only real solution I can see is re-writing a custom set of includes for each custom area. That isn't a major problem (it's quite easy to do), it's just that they will no doubt drift over time from the base set :/