When you can afford it, you'll definitely want different rooms for each element... the best rooms are allegedly pretty finicky, though I've never gotten to them yet.
Yeah, you really want a breakout room for every element. The right/wrong element penalty is basically always larger then the extra qi gather bonus.
For the non GC breakthrough it doesn't really matter cause you can just do it a few times in a row, but for the GC breakthrough it makes a very significant difference.
If you really lack enough spiritwood or whatever you can just swap the spiritwood around to the breakthrough room just before the gold core breakthrough.
Edit: one thing I've wondered - why don't we have AC units in this game? In a world that has magic materials that can produce endless heat and cold, it should be simple to just make a box with two windows, one with fire essence, one with ice, that can be adjusted to always produce a temperate room.
Like a decent number of problems with this game, this one is just fixed with what amounts to an AC mod. Its uh... fairly cheaty (aka, a tiny 2 spirit stone building lets you keep a 400 tiles room the exact same temperature the whole year), but it removes lots of micro so its worth it.
It also takes something like 3 days for qi gathering to reach max effect, so you can't just pop up a room and try to breakthrough.
It takes 5 days on a linear scale (eg. 1 day is 20%, 3 days is 60%). Again, for the non-GC breakthrough it isn't *that* important to have it get to max, but if you stick everything there then break through right away all that fancy qi gather stuff you stuck there is 100% useless.