Bazel's opinionated nature is it's blessing and curse. If you follow it's rules (fairly simple, internally consistent, and well thought out), it's amazing, and you need think a lot less about "where does this file go?", etc. If you don't have all those rules in your head, or if you're inconsistent about them, it's a nightmare.

Thankfully, it's a nightmare that can be fixed, and it behooves you to do so: Bazel's simple artifacts and build speedups are well worth the time you spend converting to it.