Seems common sense to me, thats exactly what we do too, and did at my previous outfit.
Not sure about the TCAS thing, will have to look into the manuals etc more closely, but I was under the impression that the Transponder was always referenced to 1013 regardless of what was set on the altimeter subscale.
There are far more knowledgable people out there who will be able to enlighten you (and me for that matter).