Well my group simply stops dps at certain times to avoid skipping phases. But yeah it's annoying. You come to a new Operation and you try to do as much dps as possible and it becomes habit, after a while you get experienced and have to try to make less and less dps, or get punished by bugs... makes no sense....
The thing though is, increased DPS and skipping phases doesn't punish you, as long as the raiding team is flexible enough to adapt to it and respond more rapidly.
For example on Warlord Kephess in EC you can also skip, by downing the giant droid in 2 phases rather than 3. This will make Kephess come down whilst the 2 last droids appear. Allowing for a tank to pull in Kephess on top of the smaller droids, facing away from the raid. And simply having the raid nuke both Kephess and the droids at the same time. Something which only helps further speeding up the kill.
Firebrand and Stormcaller you can also pump hard enough in SM to skip DD and the tank armor debuff if the DPS plan their burst phases well.
Kephess the Undying in TFB is the same story, in SM when upon entering the last phase if you knock down the pillar at 10% and nuke with overgeared people, you can have him dead before he comes up. In HM you can already bring him down to 3 ~ 4%. A few more gear upgrades and there too you can simply skip the last phase.
The real question is, why do additional redundant phases, whilst it's perfectly possible to just pump through them without it running into a situation where the boss can't be killed?