I don't understand who bundles who, but definitely there are three copies of the same thing. Symbol _ZN17EnvelopeGenerator13sustain_levelE@ (32-bit UNIX - System V Intel 80386) present 3 times libresid libresid-builder /media/tinderbox/usr/lib/lmms/libsid.so Symbol _ZN17EnvelopeGenerator16writeCONTROL_REGEj@ (32-bit UNIX - System V Intel 80386) present 3 times libresid libresid-builder /media/tinderbox/usr/lib/lmms/libsid.so Symbol _ZN17EnvelopeGenerator17writeATTACK_DECAYEj@ (32-bit UNIX - System V Intel 80386) present 3 times libresid libresid-builder /media/tinderbox/usr/lib/lmms/libsid.so Symbol _ZN17EnvelopeGenerator19rate_counter_periodE@ (32-bit UNIX - System V Intel 80386) present 3 times libresid libresid-builder /media/tinderbox/usr/lib/lmms/libsid.so Symbol _ZN17EnvelopeGenerator20writeSUSTAIN_RELEASEEj@ (32-bit UNIX - System V Intel 80386) present 3 times libresid libresid-builder /media/tinderbox/usr/lib/lmms/libsid.so Symbol _ZN17EnvelopeGenerator5resetEv@ (32-bit UNIX - System V Intel 80386) present 3 times libresid libresid-builder /media/tinderbox/usr/lib/lmms/libsid.so Symbol _ZN17EnvelopeGenerator7readENVEv@ (32-bit UNIX - System V Intel 80386) present 3 times libresid libresid-builder /media/tinderbox/usr/lib/lmms/libsid.so
upon further digging it seems like resid needs to be the bundled version that lmms has contains lmms specific code modifications. The system version should not be used.
I've been working on a libsidplay ebuild that fixes bug #607672 and it's rather a mess.