I just installed v3 again on my pc. To my surprise, the issue seems to have solved itself. MusicBee now launches fine, and this is before replacing bass.dll with the modified version. I reinstalled MusicBee several times yesterday to test if it was an installation issue, but the issue kept persisting no matter what I tried.
After using v3 on my pc for an hour, I decided to update to v3 on my notebook as well. This notebook is running the exact same security software as my pc. Upon launching MusicBee, HitmanPro.Alert once again intercepted an attack by bass.dll. Relaunching MusicBee kept producing the same error, and so I replaced bass.dll with the modified version you linked. This modified version fixes the problem: MusicBee now launches and works fine. Upon placing the old bass.dll back, out of curiosity, the problem reoccurs. I tried to reboot my notebook and I made sure the security software has the same version and definitions as on my pc, but I could not reproduce the magical cure that occured on my pc.
Long story short: the modified bass.dll works; I have no clue as to why the problem magically dissapeared on my pc.