You can edit the FLAC command line to include "--bps=16 --sample-rate=44100".
I can't seem to get it working. This is on a FLAC 24/96 file:
"-s -8 --bps=16 --sample-rate=44100 -o [outputfile] -"
It will convert; no problem, but the sample-rate stays the same and there would be no info on the bps at all.
On the other hand, that is the default output format for FLAC files anyway, so I don't know why you would have to.
I have mostly FLAC files that are 16/48 mostly due to my default preference for ripping CD's (not that I want to convert them all to 16/44 anyways). I think it is better that MusicBee has profiles that users can customize. So the boolean-type rule can be put to trash as MusicBee is already great with this feature.