CDAT,
As you've noted, the masses don't add up and, as presented in FR2765AFFS, the Defender should have a cargo capacity of ~32kt, not the listed ~106kt. My best guess is that the mass of the armament wasn't deducted from the running total, as the weaponry adds up to the missing ~74kt.
With IntOps having come out since the FRs publication, there's additional issues with both the design and fluff, such as the size of the ship and the stats for DropShuttle bays.
Re values for spare parts and food/water consumables, I'm guessing that you're using HMA given that they're a construct of that software, particularly the spare parts, and you won't see them in canon designs. Canon designs treat all such items as being part of the cargo. Unfortunately, like the other Heavy Metal products, HMA is badly outdated and also has some unofficial assumptions/features.
I'm also guessing that you allocated 11kt per DropShuttle bay per the IntOps rules to come up with your 38kt discrepancy. If you allocated 20kt/bay per the FR specs, you get the 74kt discrepancy I noted above.