Balanced Hackmons is an Other Metagame where nearly anything is possible, up to in-game limitations. You can assign any moves and abilities to any Pokémon—even ones already in their Mega forme—and use unreleased moves, items, and Pokémon!
Yes, if you use a Pokémon in their Mega/Alternate form, they start that way,and don't need to mega Evolve. If you have a base form holding a Mega Stone, it will still be able to Mega Evolve. Just a side note: Gengarite and Primal Groudon are banned. :P
Hope I Helped!