To start, I like the Thompson Pro Hunter platform. Mostly due to looks, overall length, easy to handle. Have had a 243 for a few years, then a custom 338 barrel, bought a 270 and 30-06 barrel last year to tinker with. In the past I reloaded everything, my die set covers about two dozen calibers. Now days I don't have much time for that so was looking for factory loads. Had a difficult time finding something that would group better than 2" in the 270 and 06 so I decided to shorten the barrels. With the scope rings removed I could only cut about 3 1/2" in my lathe so that's what I did to all but the 338 (integrated muzzle brake on it). Put a similar crown as from factory but had to deal with the flutes so I rounded them off. Came out looking nice. Yesterday I went to a friends gun range up in Oklahoma to see if this helped. Results were great, shooting factory loads I could easily get less than 1 moa, with the 243 had a group of three touching. What I found interesting is this. After reinstalling the one piece scope mounts and changing scopes around, all three barrels shot right at 6" low and 5" to the right. I expected them to all be different. Didn't take but a few shots to get them back to 200 yard zero. Not worried about anything, just found it interesting that all three after having this much work/changes done were all in the same area after. Really happy with the accuracy improvement after removing 3 1/2" from the barrels and this is my first time cutting and re-crowning.

Zeroing at 200 yards, you lost muzzle velocity cutting the barrels shorter, therefore you have more bullet drop, is my suspicion. The drift to the right, was there a left to right wind?

No wind. I know I lost some velocity, just found it interesting they all were the same 6 down and 5 right. Keeping the scope mounts with the barrels but swapping scopes I expected them to be different from each other. That being said, I was shooting some 80 gr GMX's in the 243 before cutting, used 55gr bt's after. Expected them to be a little higher.

I see a very long list of cartridges that, from a hundred yard zero, drop very similar at 200 and 300 yards.

I think it is more the barrel whip and harmonics of the Thompson Center rifles that you fixed more than the loss in velocity. There is something to them having a shorter barrels. Mike BEllm has a few hypothesis on why this happens and has has good results.
if you are into Thompsons check him out.

Yes, I agree with the harmonics, which is why I cut them down. Velocity loss isn't why they were 6 low.