+1
A perfectly valid question -the only "dumb" questions are the one left unasked.
But I guess I can somewhat quell your fears (PLEASE NOTE: medical conditions are a case by case basis; what was okay for me, may not be for you).
I have a case of flat feet. Found out from cross country last fall (Fall 2012)--> gave me tendinitis and prevented me from doing winter track that year
And for a while, I was looking into getting a prescribed set of orthodics (which are ridiculously priced BTW). Any ways, my XC coach recommended me a set, that he personally wears. It's a non-prescribed insert (from Footsmart; model is Iso Arch) that costed me about $25 - and it did the trick, tendinitis went away -- along with my shin splints.
Anyways, point is, is that I went to do my DoDMERB physical and I told them about this, and it was fine. Now, please keep in mind - my case is NOT a medically recorded case, it may be different for those with a history. The doctor who I had was even a former Army DoDMERB board member and he said I'd be fine (which I am - officially medically qualified).
Also, I know you mentioned AROTC, but for others reading this post, please keep in mind that my DoDMERB file was for AROTC as well. Had I done DoDMERB for the other branches - results may have been different.
Hope this helps!