I feel your pain
I struggled with thumb joint pain over the past couple years with it finally getting so bad last fall that I had to cut back on my riding and avoid using my right thumb for anything, even turning the car keys in the ignition and using the space bar on the keyboard! This was quite the stealth injury and snuck up slowly over time. My riding is probably about 50% Downhill and 50% XC. The conclusion that I came to after much investigation, reflection, and experimentation, was that the majority of my injury was caused by 2 years of downhilling with full finger gloves that were too small. The glove material was too short in the web of my hand and every impact I took there, the glove would pull back on my thumb in a jamming fashion (the end if the glove is against the end of the thumb and pulling back every impact). A couple other contributing factors were grips that were slightly too big that caused the thumb to be stretched away from the hand ever so slightly (ODI Rogue), and brake lever position. I don't think these would have been as big of a deal if my thumb wasn't already injured from the glove problem. They merely kept aggravating it. After getting different gloves, modifying my grips, and babying my thumb for the past 6-8 months (riding with thumbs on top of bar, minimal DH), my thumb is ALMOST back to normal. Yes, expect your thumb to take a LONG time to heal, and expect a lot of things in your daily life to keep it aggravated unless you pay attention.
Here is my recommendation on things to check:
1. Full finger gloves that are too small, causing a jamming of the thumb as I explained above.
2. Grips that are too big and cause "tweaking" of your thumb, esp. when climbing. I did one DH run with small diameter grips and my thumbs felt great, but palms felt battered. I ended up keeping my large diameter ODI Rogues since I need the palm padding for DH, but I shaved down an area under the thumb all the way down to the plastic (~4mm removed). This provided all the relief I needed, and I kept the padding for my palms. It also made a big difference when climing during XC rides, although I still climb with my thumbs on top of the bar sometimes. If you only ride XC, you could probably just use smaller grips and be fine.
3. Brake lever and hand position. If your levers are pointed too far down, your thumb will be in a bad position and will be taking direct impacts rather than the palm of your hand. The effect here is similar to grips that are too large: a tweaking of the thumb in a unnatural direction. I will also add that I highly doubt that shifters are causing anybody problems. Even when my thumbs were still hurting, shifting didn't cause much aggravation even when I was expecting it to. Examine the direction of force on your thumb from using the shifter and then from handlebar push/impact and you'll see what I'm talking about. The shifter pushes back in a straight direction with respect to the thumb while the bar pushens the thumb at an unnatural 90 degree angle.
If you have thumb pain and are reading this, don't expect any of these changes to drastically improve your pain right away. Troubleshooting my problem was difficult because my injured thumb was irritated by just about ANYTHING, including riding with what I now know is a properly tuned setup. Keep babying it and get your setup dialed as best as you can, and it will start feeling better eventually.