I don't see the problem with making the low B redundant. It should make a nice thumb rest.
An alternative, actually using the B string: If you tune to C#-D#-G#-C#-F#, the tension of tuning up the low B could be problematic. Also, riffs which 'bounce' from the C# to the G# strings would become more difficult. So, try tuning to G#-C#-G#-C#-F#. If you do that, you would always have an octave below any note on the G# string readily available. However, if you use that tuning I'd recommend you stay away from the open string and first couple of frets of the low G# to avoid subsonic muddiness.