I don't "know" what the problem is, but I can share an "I think" and what I did to fix it...
We have a remote shifter and getting the car into gear while the motor/trans is shifting around under the car can get tricky. With the stock shifter, there are rubber bushings and better leverage due to the fulcrum point.
When we put aftermarket shifters in, most of them are short throw, which changes the effective leverage point, as well as making the shift mount stiffer with a polly bushing. Because we lost some play and leverage, the alignment of the linkage becomes more important.
I think that you still need to let the trans settle even when granny shifting because the trans is still shaking back and forth after you unload it.
TQ limiters are engineered to stop the driveline from twisting, allowing all of that lost energy to get applied as usable power at the wheels. A side effect is the trans and remote shifter stay in alignment, making it easier to shift.
So yes, tq limiters are a good idea for both reasons.
I was having a problem where I would grind 2nd most of the time and just flat out miss 3rd. I, however, have not added tq limiters. I was able to fix my shifting problem for free.
I removed the nylon bolt guides on both sides of the shift linkage, left the bolts loose by 1/2 turn, and greased the linkage bolts. I used lock-tight so the bolts don't come off. This built play back into the shift assembly and allows the remote shifter to more easily "find" the moving target.
The Hurst shifter I have now works smoothly, I don't miss shifts, and the known vibration issue has been almost completely eliminated.
I have the stock flywheel and a Spec stage 3 clutch, both power shifting and granny shifting with no issues above 6500 rpms.