Please give us an update here when you are done building your hetzner beowulf cluster and let us know how it fares. I think you are grossly underestimating the system you describe.
E.g. a load balancer in front of some relatively stateless http microservices is really not going to tie you to Fly.io because of complexity. A globally distributed edge compute environment with database, RPC, varying scaling patterns, and environment certifications is probably not going to have the value prop impacted by this kind of minor pricing change though.
None of this is impossible, but when you are a small startup it makes sense to offload this to someone else and not waste time reinventing the wheel.
You won't be a small team by the time you're at a scale to need horizontal scaling. Only the biggest consumer facing/social media sites get value from that.