Hey! Thanks for picking it up. It is quite minimal of a tool at the moment (Hence the "Mini" in the name), but I do plan to add most of this. Definitely stay tuned.
The first point sounds like a bug to me. MiniMeters should restore the exact position on launch. I will look into that.
Other than the popped out modules v1.0 is going to include a horizontal, vertical, and custom layout which will hopefully meet your needs.
I will probably not create my own Stream Deck plugin, but will likely have a way to toggle features from the Stream Deck as well as other macropads and systems.