The bomb does have a proximity detonation radius now. It is a recent change and not reflected in the tooltip or patchnotes, so far as I am aware. I for one preferred it the way it was.
Strike Team and Science Proficiency have total animation lock (as does Engineering Proficiency), and Nanoprobe Infestation has a partial animation lock.
From a PvP standpoint, having the bomb set to proximity is actually quite invaluable. Not only does it trigger at the right time, it also blows up on any cloaker walking too close to the bomb. At the same time it decloaks the cloaker via knockback. Engineers don't have tricorder scan or target optics. Transphasic bomb presents the class with an interesting way to deal with cloaked players. You can't sneak up on an engineer while under cloak if they are standing next to a transphasic bomb.
Would maybe be a good idea to mention at the bomb one that it has no cooldown when it auto-explodes by proximity... couldn't hurt to get some dev confirmation if thats actually an intended feature as it seems almost to good to be true as it wasn't like that before the proximity was patched in and it can totally outdo dmg of other kits when used like that.
"(3) Bomb has no cooldown when auto-exploding by proximity - intended feature?"
If I'm not mistaken, the auto-exploding cooldown is only instant when the explosion doesn't hit anything.
Its always instant with no cooldown unless triggered manually, makes triggering em manually being the worst idea ever unless you really have to atm. And thats what makes this design feel a bit wrong actually, cause automatic triggering is easier then manually triggering yet you get punished with a penalty for doing it manually.