My experience goes only as far as phpBB2 goes, I'm still running one heavily modded one and it runs a custom template using an external file. This is only easily possible by using eXtreme Styles MOD or a similar template system (I think I have some newer lightweight one that appeared a year or two before phpBB2 support forums were fully closed).

At the moment I'm in the process upgrading to MyBB. phpBB3 just seems too cluttered to me. I've also used SMF and it doesn't cut it for me. The rest in the market doesn't answer all the needs, but MyBB is pretty good. For the moment I'm simply creating a MyBB template, but I'll eventually go deeper and do more changes. But I won't touch MyBB core files, it'll make updates too time consuming.