Sure, the explanation makes sense. But it's not really a fun mechanic, it just effectively gimps you for clicking at the wrong time. If it's just a measure to make sure you don't exploit phase too much, then by all means extend the no-fire period a bit more before and after phasing. But giving us a cooldown for not really doing anything, that's just weird. Antimatter Blaster is the worst offender here because it takes so damn long to reload.
Also: If you have two Antimatter Blasters and they're set to alternating, it can happen that you click very fast, switch back and forth between them but never actually fire, even though one of the two is readied up. It might have something to do with this weapon 'warmup' as well.