I shaved a few mm off a Qtron+ I rehoused from its gigantic container to one much less gigantic. As long as you don't break any traces it should be fine.
Battery compartment can probably just come out (de-solder and remove). Bypass might be trickier. Pedals with DI usually are buffered. I'm certain there is a way to remove the bypass control, but it may not work how you expect. DI should just be able to de-solder and come out.
Proof of rehouse: