I think the bigger issue here and your avoiding it is that it stops you from getting past some bosses without having to do them. Look I get it you dont wana have to do every boss is every mission some people do. I personaly dont care but be honest with us and yourself. You issue is that you are pullig bosses you try and sneak past while members of the group are able to get past without being stealthed. It sucks. But dont try and say its anything other then what it really is.
Every genuine stealth class has the ability to bypass bosses without ever having to use their primary stealth ability, as long as the mechanics of the instance support it. All we need is Force Cloak and its equivalent. In some instances, such as Maelstrom Prison, that will get you all the way to the final boss. In others, like False Emperor, it won't, as you are required to kill one boss or you eventually get blocked by a door.
In the current game, the mechanic serves no purpose but to annoy. I only ever notice the mechanic when I'm in a group (I seem to always forget about it until I get the red marker on me), and I'm never in a group comprised only of stealthers. And if I was, and we wanted to get by what little content can't also be bypassed by non-stealthers, we could all simply walk by the boss and use our cooldown to leave combat.
If BioWare wants to prevent players from skipping bosses, they simply need to implement mechanics in each flashpoint that require you to kill a boss, as they did in False Emperor. It never ceases to amaze me that they didn't.