"All rooms need to be cleared", for what I get, you need to kill all the possible enemies in the stage? So, in Com-Tower you'd need to go to the second room with the power thingy, don't destroy it, go clear the other two rooms with grunts that spawn, and then go back?

In this category then, the spike exploit is not allowed or would be useless? Because you'll need to kill everything to "make 100%", and that would count the scientists in Quarters too?

The number one issue and the reason why I haven't done any 100% runs is that it is impossible by the rule's definition, you can technically fully clear all levels except 1-D. The level 1-D checks if 4 specific rooms are cleared to end the level, the problem is that each of these rooms activate another encounter in the room right outside of them, so the level will always end before you can "fully clear" all of the rooms. Even if missing one room in 1-D would be allowed I still believe it would be better idea to replace the 100% category with Glitchless category instead, that would simply ban spike exploits (or it would be nice if this category was added as an option atleast). There isn't any real way of 100%ing the story mode and having to backtrack 4 rooms from the Phobos encounter just to kill 3 sleepwalker patients doesn't sound too appealing... (this is a thing you actually have to do in 1.5-D).