If the transducer is mounted on the boat with a few degrees yaw (not perfectly in line with the boat), will this cause alignment issues when generating side scan mosaics? If so, is there a way to correct the errors with processing (instead of breaking the epoxy seal on the transducer to re-align the transducer.)

Yes it will, but the effect is minimal. The worst problem with mis-alignment is poor quality SideScan as in unsharp images.

If a side scan yaw correction feature is not of interest (as a new feature request), how difficult would it be to make the correction on the DAT/SON files directly before importing into ReefMaster? Perhaps this thread should be moved to feature request. BTW - my installation error offset is 4.2 degrees clockwise.

As a feature, this wouldn't be too hard to implement, but I wonder if there is enough demand to warrant it?
If you record logs without heading information, then the (smoothed) course of the vessel is used to derive headings for sidescan mosaic. Because of this, it wouldn't be possible to modify the data files in a way that would correct it. If you are using recorded headings (which you are not, if you are using a Humminbird as we do not read them), then the simplest option would be to ensure that the heading sensor is offset by the same amount as the transducer. Better still to mount the transducer straight, of course - is this not a realistic option? Four degrees isn't a huge amount, but it is not nothing either. I am not sure how badly this would affect your mosaics, but it is probably less than the fact we are using a course instead of true heading.