I had also heard of the filters but I haven't seen a reliable source for this. It would be nice though
There's been some back and forth on this. Last I have personally heard, Docm somehow convinced them not to do it, because the hopper worked for sorting. Personally, I don't think that argument is really all that valid (IMO odd but useful behaviors should be re-implemented as official features), but that's the last I heard about it.
The allocator sends items through only when a signal hits it, instead of how the hopper always sends items through except when a signal is hitting it.
The reason for the hopper's seemingly inverted redstone behavior is because they want it to work normally without requiring any redstone.
I don't get why they didn't just implement the mod itself into Minecraft.
Copyright, most likely. The functionality of a mod can't be copyrighted, but the code is, so they have to write their own implementation if they don't want copyright issues.