Since the obfuscated files were never documented in any way, there's little chance that anyone ever developed a mod which required obfuscated MDS to work with it.
In contrast, many existing mods contain references to classes which have been obfuscated in UP3, so they won't work with UP3 (but they do with Stock 4.10.1 i.e. Modact 3).
Only a small group of registered UP3 developers was able to fix this, but then again since obfuscation is a process which always takes place across the whole set of obfuscated classes, any change to an obfuscated class required the whole set of classes to be re-obfuscated and re-distributed. Since UP3 shipped all it's classes encrypted inside files.sfs anyway, that was no big deal for the UP3 dev team, but for a single modder it just made modding UP3 impossible.
The short formula is:
UP3 in it's original obfuscated state is not compatible with modding at all.
Unobfuscated UP3 is as open for modding as any other 4.10 game is.
Best regards - Mike