Actually allergies and LPR have many, many similar issues. In fact it's very difficult to differentiate the cause of many LPR type symptom. It's muddy water, indeed. That's the struggle I have, because I have severe allergies, and many of my symptoms mimic LPR, so my allergist is always searching for the cause, and never rules out reflux.
Of course burned tissue and tooth erosion aren't the symptoms that are difficult to differentiate.
Other symptoms such as sinus issues, PND, lung problems/asthma, cough, hoarseness, etc...can be caused by allergy or LPR/reflux.
You know what I'm going to say before I say it...wait, wait, wait. It is FAR too early to decide whether or not your symptoms are residual problems that haven't had time to heal yet. Plus, as you know, reflux is still a possibility at your stage of recovery.
Hang in there!