This caught my eye because my son (civilian) has this condition as well. If you do a google search for DODMERB instruction 6130.03 you can read the criteria for yourself. Here's what I find:
h. Current chest wall malformation (754.89), including but not limited to pectus excavatum (754.81) or pectus carinatum (754.82), if these conditions interfere with vigorous physical exertion.
It appears to me (no expert here- just parent of a kid who has navigated this process!) that you may be DODMERB disqualified because you have this condition, but would have a good case for a waiver because you clearly can exert yourself physically.
Joe Papp (posts here sometimes, works for Concorde, who do the DODMERB exams) may be able to shed some more light on this.
Best of luck to you!