When I had a different TA I could not use my Disney Vacation Account. I don't know if this was her/her company's rule or if
DCL has changed but now with DU I can call, give my account number and the CM will credit my account. I can then email my DU TA (lots of abbreviations, feel like I'm back in the Navy

) to let her know there's been a credit to my account.
That said, in the past with The Other
Travel Agency I booked a couple of cruises myself after running to Target, buying a lot of Disney Gift Cards, loading my cards and then booking the military rate and using DVA myself. Saved quite a lot of $$ this way and didn't miss the OBC (one year it was a crazy amt off, something like 40-45% all said).
This is really the only circumstance I can think of when using a TA didn't make sense for me...