The US already uses different counts for apportionment and redistricting. Apportionment includes overseas military and other officials attributed to a specific state. Those persons are not assigned to any census block, so they don't count for redistricting. I don't see any reason that SCOTUS couldn't decide that persons ineligible to vote are also withheld from the redistricting count.
The order of magnitude of that discrepancy (which is unavoidable), and to a lessor extent the discrepancy between CD size of a one CD state up or down as compared to multi CD states (also unavoidable), is relatively minor as compared to the avoidable discrepancy that would be introduced by virtue of counting non citizens for purposes of inter state allocations, but not intra state allocations.
The present discrepancy is avoidable, since overseas military personnel could be assigned to their last home state address, in much the same way as some states are doing with their prison populations.
I understand that there is a matter of degree, and I am not advocating for a particular standard, but if SCOTUS finds for the plaintiffs in the question of redistricting, I think they can read the constitutional language on apportionment as a strict count of all persons in the state. Though I will be curious to see the arguments, it does seem that the inconsistency today is the use of CVAP to count for VRA purposes, but not for the overall district population.