I had to "customise" a case for my PRS-1TS kit build. Because of the angled headstock, it didn't sit in a standard rectangular strat case without putting too much pressure on the headstock/neck.
I was able re-position some of the factory padding as well as adding some extra foam and now it sits comfortably and safely in the case.
I also got some black faux fur to cover the foam, and you wouldn't notice it without a close inspection. It looks like a bought one!