[Feature]: Make repo default for setup script and similar host configurations apply for all hosts started by per-worspace Environment

### Problem or use case

Right now setup script and similar features are unusable with Per-Worksapce Environment, as every single time a new worktree is created no setup script and such as attached.

### Proposed solution

Make a single setup script apply at least for every single VM created by the per-workspace env feature, as those VMs are more ephemeral. There no issue keeping the separate configurations for permanent SSH hosts, which are mutable.

### Alternatives or additional context

Can also just make it the default for all hosts, permanent SSH hosts and local included, but this would make running on vastly different envs more difficult.
Can also pass setup and such via vm env config itself, but then these repo configurations stay useless, which doesn't seem right.

No files or tests are named. Start by tracing per-workspace Environment host/VM creation and how repository setup-script and host configurations are selected; done means the repository default applies to every ephemeral VM while permanent SSH host configurations remain separately configurable.

Written by the indexing model from the issue text.