Okay, I've got a little update. I had a chance to read the N33 document itself. It was somewhat vague/confusing and necessitated further inquiry. With a little bit of persistence and having an awesome recruiter on my side we were able to seek some clarification.
As it turns out, Navy Med made a phrasing/clerical error in their letter with regard to the reason as to why I am disqualified. I am still disqualified, but not because of the depth perception issue like what was originally written. They do in fact accept depth perception retests, and had accepted mine as being within the standard, but they accidently included it in this letter as the sole reason for my disqualification. The real issue is that my right eye according to MEPS was logged at 20/70, which falls outside the 20/40 SNA standard.
A retest is available for this, and I know from experience with optometrists and personal testing that I can hit 20/40 vision in my right eye (just barely). But the risk here would be passing the retest and not hitting 20/40 at OCS or my pre-NIFE flight physical.
TLDR: Navy does in fact still accept depth perception retests. If you need one, go get one.