How to get rid of gitdir reference in submodule?

Lets say I have this workflow:

1. Has a git repo without submodules
2. Just using git clone to clone another git repo inside
3. Afterwards adding the repo as submodule by doing git add on existing repo

In that case the tree structure is the following (lets call it Structure-no-gitdir-pointer)

- main_repo
  - **.git/**
  - some_files
  - submodule
    - **.git/** (note that this is a directory, containing all the info like branches, config,  description,  HEAD,  hooks,  index, ...)
    - some_files

If I push the project and clone again with all the submodule, what I get is following (Lets say its Structure-with-gitdir-pointer):

- main_repo
  - **.git/**
  - some_files
  - submodule
    - *.git* (points to `gitdir: ../.git/modules/submodule/`)
    - some_files

I would rather like to maintain Structure-no-gitdir-pointer in the cloned repo since I am doing some volume mapping with submodules and I lose all git references. (I don’t want to map the parent module itself).

Any way to do it more or less automatic?

I have found this thread (Migrating a submodule’s gitdir to ‘in-tree’) which concluded to do things manually, not a fan of that approach.