Yes, but I saw why it can't work after your message. Somehow I forgot to implement this. In the moment the custom controls just checking for Visibility and for AutomaticInvalidation. I will write a patch to make It work in the next iteration of MonoGame.Forms.
You could try to turn off the AutomaticInvalidation on your main window. Then no control events are getting raised and also the Update and Draw methods won't get updated anymore.
This could also resolve the issue with different matrices.
Normally you wouldn't have such problems, when using multiple controls on one Form. I have not tested the use case of having multiple Forms together with custom render controls. MonoGame.Forms works best when hosting multiple custom render controls on Panels for example.
When working with several custom controls in different windows (e.g. floating windows), then the DockPanelSuit will be a great help. I use it myself for this purpose and during the development of MonoGame.Forms I always made sure that it works flawlessly with this library. So I can really recommend it in this case.
But if you want to create a simpler editor environment I recommend having multiple custom render controls in Panels and Tabs on one Form only.