Fix multi-function project kubernetes deploy command

[f1x3d]

Issue describing the changes in this PR

Resolves #3585

This was tested with a repro project, see the results before and after the change

If someone could provide me some guidance, the same steps can be added as an E2E test directly to this repo

Pull request checklist

• My changes do not require documentation changes
  • Otherwise: Documentation issue linked to PR
• My changes do not need to be backported to a previous version
  • Otherwise: Backport tracked by issue/PR 'func kubernetes deploy' hangs when using NET5 dotnet-isolated #2556 (the kubernetes deploy is completely broken for dotnet-isolated in v3)
• I have added all required tests (Unit tests, E2E tests)