My advice would be to use a normal live iso for development instead of the dedicated m-a iso. They all have m-a on them but the full iso will give you a working desktop to work out of it.
Sure, you can exit and restart m-a. It is ultimately a shell script. Just run
sudo manjaro-architect from a terminal or TTY.
When I was making changes to architect I just copied and pasted a couple of scp lines that copied the working files off my development workstation into whatever vm or physical box I was using.
When I was closer to the end of my testing I started building a package on my workstation and then installing it on the vm.
In your case, you could test your initial changes on your development workstation. m-a can be installed and run on any manjaro install. If you are mostly changing the menus initially, you could test that without breaking your system. Just don't use the "format disk" menus for your testing.
My best advice would be to just start making changes and see what happens. It is easy to overthink it so sometimes it helps to just get started.