Puhh... tough one. I could only try to scramble some workarounds together similar like "Open all Favorites in a folder" (macro Favinia) to get a list of the files. Meaning to get a file list of a folder, needs to open that folder as a webpage in the browser, with all files appearing as links, of which then a javascript can make a list of. That list of filenames would be stored in an ini-file between sessions. This initial get-list-command would have to be executed once when you add new scripts, started manually.
Then each time when a webpage has finished loading, the macro would read the content of the first userscript, crop the chapter with the @include-lines, compare if the current domain appears in that text block anywhere, if yes insert that file. Then it takes the next file, looks if current domain is in it, etc. etc.
Sounds like quite a performance eater to me, depending on number and size of files, and am sure a pro could write something that works a lot faster and with probably much slimmer code, and myself probably just not being the right person for this.
Anyway, the next prob is, macros can only insert scripts after a page has finished loading, not sure if that's always sufficient.
Further prob, how to disable single scripts?? Hm, well okay, just move them out of the folder so the macro finds no content... It's all just workarounds really, more or less working and awkward...
And another prob, would it work at all??
Have you tried if your scripts work with StyleonMini, especially those bigger as 32kB, and especially in KM75??
And when I'd finally have it halfway working, someone will come with a fixed greasemonkey that does it all much better