This is a tough one. I'm curious to hear what others do, but I've migrated away from the RPTC pinches because of this issue. Maintaining externally rotated shoulders while hanging on the RPTC pinches places a lot of torque on my thumbs; internally rotating my shoulders (elbows out) removes that thumb issue but creates soreness in my shoulders. This didn't used to be a problem, but with increased weight over the past couple years, it's left me a little sore and didn't seem worth the risk.
After recreating the pinches on my DIY woodboard (took a while to get it right), I realized that it's hard not to fake by pressing. I never knew, how much actual pinching (thumb strength) was going on. Soon after I found pinch blocks, and started to lift stuff with them - surprisingly hard to lift moderate weight with them.
I'm using the Rock Prodigy hangboard and I was wondering if anyone had any experience with what would be the best body position for this grip type.
Same as the other holds; shoulders contracted down and back away from ears, elbow forwards a bit (as mentioned above), elbows slightly bent.
Since I'm usually removing bodyweight on these, I haven't had any issues with shoulder pain. If you do have shoulder pain, even with shoulders contracted as suggested above, you might want to move your holds closer together.
Overall I've enjoyed training on these pinches, and don't think it's necessary to supplement them with other pinch grips. However, it's easy to make your own weight-lifting pinch grips -- just hang some weights from a piece of 2X4 or 4X4 and pinch the wood at your side. Or attach said wood grips to a cable on a cable machine in a gym.