Looks like java.nio.file.path is going to be added in Android O (API 26): https://developer.android.com/reference/java/nio/file/Path.html
Hmm, that's sort of good news, and provides a tiny bit of hope, but it'll unfortunately mean that the zips would only run on a system with an O ROM or above.. so full support would lapse from Lollipop to Nougat.
I guess we could include both sets of jars to make it work from ICS to KitKat and then O+. I have had reports that some things will work on Lollipop and Marshmallow (my PoC linked in the OP for example) with the old jars, so we could attempt to use them in those cases, but it seems like it's hardly full support for those releases without the newer jars - very hit-or-miss, which wasn't what I was hoping for with this project.
It also might solve the errors for bak/smali but not the ones with Apktool; as @iBotPeaches suggested they stemmed from a few things. I'll have to reevaluate things once I get an O ROM to test on.