I've successfully managed to work around all the app issues after the fact by extracting the erroring APK libs Lollipop-style into the system APK folders, and following a reboot things start to work normally again. I'm going to try some things to see if I can make just the APKs function as expected, but either way I should be able to fix up some form of Marshmallow support for the next version.
Edit: zipaligning the Play Store originated APKs didn't do the trick like I'd hoped, so I guess I'll implement the workaround as I mentioned above; I'll see if we can optionally delete the libs and zipalign like on Lollipop to save the space too now that the internal APK libs are apparently useless for our purposes.. :good:
Edit 2: Damnit, started running into the SystemUI FC issue.. First with my zipaligning test, and now with my automated lib workaround.. Weird that it didn't happen the first time, going to see if I can figure it out..