Hi @Celian_GTRD,
I have done a similar project myself and it works just fine.
GNS3 is a network emulator where you can emulate entire network architectures including switches, routers, hosts and other various components. And by emulator it is meant that it emulates 100% of what you'll see in the outside world, so there's no difference. Running OpenZiti inside GNS3 is no different than running it outside.
If you’re just getting started, I’d recommend familiarizing yourself with GNS3 first , how it works (e.g. nested virtualisation / Qemu etc ...) and what it can do. Once you’ve got the hang of the basics, you can start building your project just as how you'd build it outside of GNS3.