I agree. Personally, I never use the sub INIT {} form, I always do the block form INIT {} it makes them look (a little) more distinct in the code.

But how do you go about actually calling the CHECK and INIT blocks?

I would likely move the code in INIT out into another sub, and have INIT call that (allowing it to fail in mod_perl since it only produces a warning, although this would not be okay if you had set the warnings to be fatal). Then check for the mod_perl env, and push a handler that calls the sub-formerly-known-as-INIT. This is of course a simple and untested approach, but it certainly a surmountable problem.