Yup, it's a major headache for suppressor manufacturers. In terms of pure alignment, if you think of it as a degree problem that's a good way to picture it. A muzzle brake extends about 1-2" past the crown of your barrel usually. A suppressor is probably extending about 5-9", depending on the model. Any janky threads are going to become a problem given the increased distance that the bullet has to travel prior to exiting the suppressor vs a brake.
Also in a less catastrophic way, the threads can be too shallow or too long. My father's Tikka CTR factory threads are 5/8-24 but they're deeper than they should be so the TBAC CB brake I had put on it would bottom out with some empty thread space still to go. Had to have my gunsmith use a small spacer to get it to sit right. It was never a problem when he was just using an Insite Heathen muzzle brake because the brake is user indexable and can compensate for that with the indexing nut. All sorts of things can be wrong with muzzle threads and if you're using a user indexable muzzle brake (as many people do) you'd never know. That's why since I use TBAC suppressors, I make sure to get threads done by people that TBAC has communicated with as to how to do it right.
I'll post the links below so you don't have to take my word for it. The third link is for a couple of videos TBAC has on threads for suppressors if you're interested. He goes over some common threading issues and the problems they cause.
https://thunderbeastarms.com/tech/thread-specifications
https://thunderbeastarms.com/threading
https://thunderbeastarms.com/videos?s=thread