Today I decided to write a little wrapper program for the Papyrus compiler so that I could 1) keep script sources in separate folders and 2) use Creation Kit with Mod Organizer in order to keep "\Skyrim\Data\" free of loose scripts.
At the moment the only feature of the program is modification of arguments sent by CK to the compiler so that it would be possible to pass along more complicated arguments to the compiler. However, if there are any additional ideas or requests for features that you would like to see implemented, then I'll consider them. Or you could just implement them yourselves since the source code is available under the MIT license. I would appreciate it if you made any modified source code available as well, but it's not a requirement.
Documentation on how to use it and a copy of the whole thing are available at the https://github.com/Kapiainen/Advanced-Papyrus.