Yep. There are no guarantees with neck/body fit. It's good to know how to make necessary adjustments and such to finagle the fit for the best set up/performance.
I have put together partscasters that required neck heel and/or pocket and/or bridge saddle modification to work properly. My parts Tele, "Party," was testament to knowing how to assemble and tweak random wooden parts to work as they should-it required some shaving and sanding on both the pocket and heel. Same with a couple frankensteins my friends and I put together in the 80s: most notably putting a late 60s Tele neck on a Hondo Flying V body. We had to do some neck pocket sanding, redrill the neck screws and shim up.
I have also put together partscasters that screwed together and set up perfectly, like it was an intentional assembly from the factory. T42.5, FoundRiot and RicRiot were like this, (no surprise) as it was just swapping bodies and necks from the same era that were known to be compatible. Barry Covidcaster was a pleasant surprise, but the Eden body did pattern off of a pretty standard, 60s Strat specification and it was a legit Fender neck for baritone conversion.