Hey, this is crazy close to what I'm doing with the
Metroid Generator; how exciting!
I'm doing mine in code mode, but it would be entirely possible for it to be done with blocks as well. A few thoughts come to mind;
0. To answer your question; putting it in a starter scene is fine if you're going to do some generation there. My plan is to generate on a "new game" trigger; perhaps with options to tweak the settings while doing so if desired.
1. Since each room is a pre-built scene, if you don't need a dungeon map then you can send the player to any of your pre-built rooms any time they go through a door. If you want it to feel logical, then just make sure you have every door save which scene it should be going to (presumably with game attributes, so the data doesn't get lost on scene switch). If you want it a bit more maze-like, then you could just go to a random room every time or at least some of the time.
2. If you do need a map, or at least the ability to have the rooms fit into your grid (as in the example), you could do something like what I am doing. In my case, I create rooms based on a 2D grid (a list of lists) by having an algorithm make one after the other in a chain with some checking to make sure they don't overlap.
There are lots of examples of things like this online; the bottom of
this ProcJam post has quite a few links to get you started.