So, I created a custom Ice/Poison Beedrill form, and with it, a Ice/Poison Mega evolution. With the held item for mega evolution set as Beedrillite, I tested it, and the Ice/Poison Beedrill mega evolved into the regular Bug/Poison Mega Beedrill. I confirmed that this was the actual regular mega, and not just it using the regular textures, by having it get hit with Metal Claw and seeing that it did not receive super effective damage.
I then tested it again, this time setting the required mega item as an opened Mosaic Mail, and it successfully evolved into the custom Ice/Poison Mega Beedrill (which I again tested by hitting it with a Metal Claw, and it did receive super effective damage).
I tested it a third time, now setting the required mega item as a Venusaurite, and this time it evolved again into the regular Mega Beedrill.
I did more tests with some more items, namely Rock Memory and Power Anklet allowed it to successfully mega evolve into the custom Ice Mega Beedrill, while Metagrossite and Pinsirite made it mega evolve into the base form Mega Beedrill.
So, in summary, I created both a custom Beedrill and a custom Mega Beedrill. When the required held item for mega evolution was set to any mega stone (tested Beedrillite, Venusaurite, Metagrossite, and Pinsirite), the custom Beedrill would mega evolve into the regular Mega Beedrill. When the required item was set to any other item (tested Mosaic Mail, Rock Memory, and Power Anklet), the custom Beedrill would mega evolve into the custom Mega Beedrill as intended.