Of course you can!
And the only thing needed is a boot manager, like xboot or stoop.
You just select which files to run at the bootstrap, and you are done.
Of course, you need to know which files are required to boot each system, but being an Atari user, you already know it
I don't own Magic, but I currently boot
MiNT (latest alpha, with N_AES)
MiNT (last official, with XaAES)
MiNT (last official, with MyAES)
the same as above, in 030 mode
plain TOS in diferent sets.
I keep all these different bootstraps for experimenting and benchmarking purposes, I usually boot MiNT+MyAES, but I am finding my way through MiNT+N_AES.