Hmm, first time we've even heard anyone here trying to run DOSBox on Raspberry Pi, IIRC. Based on what you've said it sounds like a DOSBox emulation bug specific to that hardware/platform/port. It makes sense that there would be a difference between Lemmings 2 and pre-Lemmings 2, as the pre-Lemmings 2 DOS games only uses the OPL2 FM synthesis features for sound and music, whereas Lemmings 2 uses other, more advanced SoundBlaster features for sound and music IIRC, at least on the default settings. It makes sense that there could be emulation bugs affecting one but not the other.
One thing worth mentioning is that even on DOSBox on PCs, IIRC at least on some versions (not sure about current versions), setting the CPU Cycle setting too high or to "max" could interfere with the game's sound hardware detection programming resulting in no sound. I don't think that's the problem here though since you said the same dosbox.conf file doesn't repro the problem depending on the setup. Nevertheless, if your configuration has CPU Cycle set to a high value, maybe try lowering it and see if it might help. On PCs I think the default is something like 3000 or 6000, which is quite low but the game still runs fine even on such a setting. On PCs you can go quite a bit higher than that default without hitting the sound problem.