Thank you everyone for the kind commiseration with my situation. After a week and a half of my leadership being beyond stellar and fighting for me and for answers, I have some clarifications.
Apparently, the reciprocity for clearances between departments goes away as soon as there is any mitigating circumstance. So while my clearance is perfectly fine within the DoD, any other department would review it independently for clearance and decide whether or not to grant a waiver. That is not a one time thing, however, and would have to be done literally any time I PCSed to a non-DoD unit. Every NIOC is owned by the NSA for crypto, and for 1810s the vast majority of the programs are actually owned by some other stakeholder. So it was highly doubtful to the interviewer that I would have much value as an 1810 due to the shear number of places I could not go. Even going between NIOCs would require a new waiver every time.
The fact that this was determined so late in the process somewhat enraged my reporting senior and his deputy, who happen to be a CAPT FAO and a CDR 1830 respectively, and apparently kind of called the 1810 community manager and guilt tripped them hard.
So, 1810 is out for me. However, my leadership argued them into granting me an exception to be allowed to apply for 1830 at the November board. I was able to get it thrown together, plus it up with another LoR and a couple more CDR 1830 interviews, and turned it in today. So here is to hoping I will get another chance at this as an 1830!