Wheel Alignment vs Sprocket Alignment
 

I have one of these motion pro alignment things you use to check alignment by clamping on your rear sprocket. Not sure if I ever used it with the stock sprocket but after installing the CSC 47T with included spacers and longer bolts I noticed a discrepancy. If I align the axle with the sprocket the wheel is noticably out of alignment and the notches on the swingarm are an entire notch out from each other. If I ignore the tool and align the wheel then the notches on the swingarm are perfect but the sprocket is noticably out of alignment.

Do I align the wheel, align the sprocket or split the difference?

I would say the sprocket. Then test if the bike goes straight.

I rode the bike with sprocket aligned, then realigned to the wheel. Can't say either way was noticable. I know from experience that a misaligned tire wears very fast. How crucial is sprocket alignment?

Probably your tires will be aligned when you align the sprockets, but with Chinese you never know. If sprockets are not aligned, chain and sprockets will wear faster.
You can more easily feel if the bike pulls to the side if you remove the hands from handlebar, at a moderate speed.

Align the rear wheel. I've read several things about the TT250 sprockets not lining up. Some folks have remedied this by flipping the rear or front sprocket.

If I remove one set of spacers it might be slightly better, have to try I guess. I wonder if the original sprocket was out of alignment or if it's an issue only with the aftermarket sprocket.

I would ensure that the front and rear wheels are aligned. The countershaft sprocket has some lateral play, which will compensate for a chain that is not perfectly aligned (to a point). I agree that you should experiment with spacers and/or flipping the sprocket to get closer.

So far the paint or powder coat on the side of the teeth on the 47T sprocket is still totally intact. If it was badly out of alignment I would have expected at least that to wear off by now. Removing one set of spacers wont change the angle but at least it would be a little closer to aligned.

Just got my 2020 TT250, and got right to work on changes after the first 25 miles.

I put a JT sprockets 45 on the rear, and used NO spacers. Chain and wheel align perfectly!

I believe the stock 50 T sprocket with the “dish” is actually OUT of alignment.

Did a quick heat gun hit on the chain guard to open it up a bit as well, and did need to lightly sand out the inner hub circle on the sprocket - just enough to remove the paint.

Great upgrade, fits perfect, all aligned.