SCons: Convert remaining run_in_subprocess to env.Run

[Repiteo]

A handful stragglers making direct calls to run_in_subprocess were still in the repo. Replaced them with calls to env.Run, like everything else. I believe this means that every single log output is now accounted for, so verbose=no will be a sea of uninterrupted blue.

[akien-mga]

Seems fine. Should we then remove run_in_subprocess from platform_methods if it's no longer used?

[Repiteo]

Nah, it's still used; the difference is that it's now used by Run in methods exclusively. It's possible that it might not be needed in the future if the build flakiness that caused it in the first place has been addressed, but that's something that'll need to be looked into more thoroughly

[Riteo]

Looks fine and dandy :D

[akien-mga]

Thanks!