1.
Not intentional, fixed in latest commit. Feel free to re-roll the Encryption Constant for >=gen6 PKM, and copy the PID to EC for <gen6
Future iterations of the code will consider the original generation (if it was imported up) when doing this copy.
2.
Gen6 Event Pokemon should never have an OT Friendship other than the base friendship.
When you inserted the Pokémon with an old version of PKHeX you didn't specify that the current handler was the HT not the OT, hence the OT friendship ticked up.
The latest versions of PKHeX automatically sets the current handler value when you put a pkm into a save file.