Ultimately I think there shouldn't be any custom teams or leagues. If this were a bigger game, I'd be fine with having a separate category for times achieved with a customization, but at the moment I don't see that as necessary. It's not uncommon for sports games to allow you to build a custom team, and my opinion is the same for all of them.
Here's a solid example of what a custom team can do, along with my thoughts about it. Basically, I think custom teams can get you a very good run very quickly but the lack of speed points to distribute is a giant obstacle towards being possible to contend for WR times.
My first run with Heroes against a custom team was 4 seconds green at the 9-hitter bunt "split". Probably a true 'best run ever' split, even. It significantly trivializes bunting to face a pitcher with zero curve/sink ability, every pitch is perfectly straight (and max velocity too).