I’ll be back home on Monday and will help more at that point.
As far as building goes, that’s flyctl logic, and if we identify common use cases that logic can be improved.
As far as runtime goes (including secrets), ultimately what is build is a ContainerConfig, which you can pass directly ( Using Containers with Flyctl ) or (if we find a reasonable mapping) we can build a ContainerConfig for you from a compose.yml file.