Yes. For example, if my players are facing monsters with a +3 bonus to hit and the same bonus for damage, and that is all they ever see for a few sessions, they will really pucker when they go up against the demon mage with +10 to each. They will feel that difference regardless of the room target, and that enemy will feel meaningful. Characters with low armor will really pay a price, but characters with high armor have a chance.
Meanwhile, the room has these slithering snakes everywhere. Whenever one gets close, the players must make a Dex save against the room target to avoid taking automatic damage. Unless a player is the thief or the archer (because others won’t have points in Dex), these snake guys are serious trouble. The tank, with a high str and armor, will normally crush most every bad guy up close, but now he’s in trouble with these little guys. Meanwhile, the thief gets a chance to shine avoiding these attacks.
See the difference mechanically and how they feel different? Using the latter method is my favorite prized pony to challenge higher level groups, as they usually have a couple of low stats. If it’s not snakes with Dex saves, it’s mind controlling fungus with Int saves, etc. But if I used only saving throws (players rolling against the room target), I lose this variety as a DM. In that same fungus room, they may or may not be going up against a deadly basilisk with a high to-hit or damage bonus, which is separate from the fungus save.