I don't expect that there is a way this problem can be fixed that's worth any negative side effects of Project64 as a whole, but no emulator-plugin-configuration combination will fix those damn alpha issues in Bomberman 64. The game is, by far, still playable, so don't worry about it if it seems too much to work on.
I did think of one suggestion for this already fine emulator, but let's see if anyone likes this idea better than I do.... Maybe there should be a "Multiple ROM Images" dialogue? For example, when an user (why do they say "a user?") opens a ZIP or 7Z archive with multiple ROMs in it, Project64 should come up with a dialogue asking which ROM from the archive to open? This could be useful if an user organizes different country versions for the same game in each archive. Like, opening Super Mario 64, but the archive has a US and European version of the ROM inside the archive, so it asks which country version to open? So maybe just enable choosing a certain country version of the game within the archive instead?
A small idea that could be helpful to few, but just throwing this out there.