If each of your tenants need their own fly.toml configs, you either have a choice to deploy them as separate apps, or deploy them as raw “Machines” (1, 2) – as opposed to using Apps v1 or Apps v2 – with their own fly.toml configs. Note that Fly apps (and Machines) in the same org can discover and talk to each other over 6pn and so, you may want to carve out one 6pn network namespace per app (3) or, per cluster of Machines belonging to one tenant, if that’s even possible.
Also, billing might get tricky as you’d have to keep track of resources consumed by your tenants yourself (at least until Fly complete their billing API implementation, if they haven’t already; 4).
All that said, there are others (5) doing multi-tenant on Fly (I don’t), may be they’ll chime in.