Yes, it is a fairly subtle difference! They suit more or less the same applications - The Mother's Milks being Tim's interpretation of the '60s sound without being concerned with vintage authenticity, then the PAT Pends being there for those that want as close a reproduction to the genuine thing as possible.
To my ears, I'd describe the '63s as a bit more focussed and possibly more open, where the Mother's Milks are slightly woodier and percussive. In my opinion the differences aren't large enough to say they specialise in wildly different sounds. I'd happily put either in more or less any strat, though if you were to press me, I would probably favour the '63s in a brighter instrument.
The introduction of the '63s was more to satisfy those looking for a vintage-correct set than to fill a unique sonic role in the range :)