It all depends on what your goal is. The WON version is automatically capped to 100fps (except for in Blue Shift where it’s capped to 72) but has uncapped bunnyhop speed and Steam version has uncapped fps but capped bunnyhop. NGHL has both uncapped fps and bhop but is an unofficial build. So does Bunnymod Pro.
You are obviously free to do as you wish. The only case in which there are rules in place is if you want to submit to the leaderboards for single-segment/real time attack runs. In order for a run to be accepted there, you must either use an official version (WON or Steam), or if you want to use NGHL or Bunnymod/other mod you need to replicate the traits of one of the official versions so that you’re not combining the features. The most popular way at the moment is to use NGHL or Steam with Bunnymod Pro installed as a separate mod, then set your fps_max to 100 to replicate what the WON version is capable of. Of course in Bunnymod Pro there is also an option to play with capped bunnyhop speed (see here for commands), which would mean you could use however much fps as you want; replicating what the Steam version is capable of.
Bunnymod Pro is a mod that can be installed to NGHL or Steam. NGHL is a non-steam build that runs as it’s own client.