Pinch harmonics become a little more difficult when the tension of the strings goes down, but that’s something you’d get used to after playing them for a while. By losing the “Cream” that you are referring to, I think the smaller gauge gives you a little less output, so the pickup is affected. If it was a full set, then both the B and G strings are smaller, so less tension, less output, and believe it or not, you would probably benefit by doing slight adjustments on the pickup heights too, since the strings all are now a couple of thousandths further from the pickup.
Changing the gauge also slightly changes the intonation, did you happen to check that? Having all the strings in tune with each other helps the fatness of the tone by getting the harmonics helping each other. The nut slots now also have more room than before.
If the heavier gauge is not uncomfortable to play, I’d stick with that. I always got better definition with thicker strings, and you can hit it a little harder without having too much excursion.