1: Skinning Plus! itself was possible long before 4.50 introduced skinning Messenger, during all that time it was never really used, with a few rare exceptions. If suddenly loads of Plus!-only skins came in i might consider splitting them to a separate category, but up to now none was ever submitted, and i don't see this happening soon either. The demand for Messenger skins is much higher than Plus!-only skins, so skinners rather make a Messenger skin, and i can't blame them.
2: Bundling a script with your skin and automatically importing that script when the skin is imported shouldn't be that hard to implement, but it's probably more a security decision. I believe Patchou made a reply about it somewhere. Skins in it's current form are pretty harmless, all it could do is make Messenger unusable, but nothing that can't be fixed by deleting the skin or running the recovery wizard. When scripts can be bundled with skins it can do anything, including messing around with your system, stealing password etc., which can give Plus! skins a bad reputation. The examples you give are useful, but if these add real value to skinning it's probably better to introduce them as a skinning feature.
I didn't like skins in the old days because they came with dodgy .exe installers, bundling scripts with skins kinda brings that back (although that's a bad comparison
).