TMJ and Invisalign

You stated that your bite comes together perfectly. 

The body is amazing. Your muscles can adapt to even some of the worst bites. Only a dentist who is trained in occlusion and TMJ can truely determine if your bite needs changing. 

Depending on the dentist these changes can be done with regular braces or Invisalign. It is considerably more difficult with invisalign and it is unlikely that only doing the lower will work. Either way, once the braces/invisalign are done, the dentist will still need to do some adjusting to your bite.

Not fixing your bite can lead to more issues, even when the pain goes away the damage can be continuing.

You were right to be concerned.