`nogo`: Issue with `isolated` extension and separate `go.mod` with `tools.go`

When using a `tools.go` approach and having a separate `go.mod` with a separate `go_deps` usage via `--experimental_isolated_extension_usages` as documented at: https://github.com/bazel-contrib/rules_go/blob/v0.53.0/docs/go/core/bzlmod.md#depending-on-tools, my project fails.

I intend to add more details to this issue but for now I have a reproducible: https://github.com/albertocavalcante/tools-nogo-issue

And these are the error messages: https://github.com/albertocavalcante/tools-nogo-issue/blob/main/STDERR.md

Start with the documented “Depending on tools” section in docs/go/core/bzlmod.md, then reproduce the failure using the linked tools-nogo-issue project. Compare its separate go.mod, tools.go, and go_deps setup with STDERR.md while using --experimental_isolated_extension_usages. Done means the documented setup no longer produces the reported errors.

Written by the indexing model from the issue text.