Okay, so two really big things:
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You're confused a bit on how network routing works. If you're building something that bridges multiple networks (local + VPN + VPS), you need to know about how to route things to different places. You're dealing with 3 networks at this point.
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You might be misunderstanding how "zero-trust" and local networking fit together. Right now you have some local machines at least, AND a router. You don't need all of your local machines to individually bridge a gap to your VPS, you want it the other way around.
If the majority of your machines are local, then make that your hub. Everything else should be a client. Adding all these individual nodes to routes in a mesh network makes absolutely no sense, and will definitely cause routing problems, if not something like ARP poisoning (we can't see your config).
Just make the remote machine clients to your local network and be done with it.