Follow-up from "Move init_tools script into gitlab rails"
MR: Pending
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## Description
The following discussion from !191251 should be addressed:
- [ ] @cwoolley-gitlab started a [discussion](https://gitlab.com/gitlab-org/gitlab/-/merge_requests/191251#note_2508254604): (+1 comment)
> **thought (non-blocking):** There's some more elegant ways to handle the sub-process execution, such as `Open3.popen3` (https://docs.ruby-lang.org/en/master/Open3.html#method-c-popen3).
>
> Could we make a quick TODO and follow-up issue to consider converting this to `Open3.popen3`?
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## Acceptance criteria
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## Implementation plan
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