Well, for stealth you best cloak after the boss fires his weaponry. Stealth gives a very good dodge bonus, allowing you to dodge his missile weaponry. Hopefully, by the time it recharges you cloak has recharged as well.
It is why it is better not to use your cloak at level 3 against that level of boss unless you are doing emergency repairs.
His weapons don't charge while the cloak is up, so the first form this doesn't matter. His special abilities however, DO, and for form 2 you want to use the cloak to avoid the drone swarm, and for for three you want to use it to avoid the super weapon, both of which don't last as long as a single point cloak.
You're still better *off* using max cloak, at least for the first of each of these, but you need to use it
early - something that's difficult for people to do unless they've got a lot of experience fighting the boss and know how to time it well. Max cloak will allow you to dodge, for example, the initial missile volley AND the first drone swarm, and the max cloak pushes the missile recharge time much closer to the next swarm which might allow you to dodge both again.
But there's a good deal more micro going into that - 1 pip of cloak and just taking the missiles on the chin is a lot easier (or, if you have high shield and decent dodge, max cloaking to avoid the missiles and taking the drone swarm/super weapon on the chin).
Also, to maximize recharge rate, you want to fire all your weapons at *just* the right time to end the cloak immediately after the swam ends/weapon fires. For the drones, often a bit before to be honest, depending on weapon enemy charge rates, since you can usually weather a couple seconds of drone with no damage as long as the enemy isn't firing their main weapons on top of it.
The cooldown on the cloak is the same no matter what, the reason for 1 pip is that it *ends* the cloak sooner.
I'd also recommend dumping stealth weapons before the final boss unless you're running rapid fire stuff (Ion 2, Vulcan, etc.) and counting on sustained pressure, since being able to sync fire and immediately end the cloak, at just the right time, is the easiest way to insure you have it ready for the next bit.
Although obviously, yeah, if you've got damage or guys need to heal, cloaking at max really gives you a chance to catch your breath... but it means you're more likely to eat the next volley of the enemies special weapon, so it's a risk/reward scenario.