I've been using this project for all my Drupal sites and I noticed one thing that bothers me.
When requiring new modules locally or running composer install on production (I use git for deployment) the following files will always be overwritten.

I understand that this is done on composer create-project and composer update but why when requiring new modules?
Is there any way to prevent this?
I was sure that this didn't happen in the past so I explored a little further (thanks Zan for helping me) and found that this happens since drupal-composer/drupal-scaffold was changed to drupal/core-composer-scaffold. Related issue: https://github.com/drupal-composer/drupal-project/pull/522
Are there any downsides if I keep the old (drupal-composer/drupal-scaffold) package?
I found a solution but this will also exclude these files on composer update: Excluding Scaffold Files
I'm not an expert in composer but is it possible to somehow disable exclusion on composer update?
Maybe use the approach covered on the same page under Altering Scaffold Files. By that you always use the core scaffold files and apply your own patches to make them look like you want. When you $ composer update and there are changes in these files you'll recognise it by your patches failing to apply. You then can review and readjust your patches accordingly. https://drupal.stackexchange.com/a/290990/15055
But let's continue this discussion somewhere else. It's off-topic here.
Relevant core issue: "Avoid re-scaffolding unchanged files (and printing scaffold file information over and over)" https://www.drupal.org/project/drupal/issues/3103090
Thank you both!
I also found this issue: https://www.drupal.org/project/drupal/issues/3092563
Scaffold files should not be modified in Composer-managed Drupal sites; instead, users are expected to use "append" or "patch" capabilities to add their custom content to the Drupal-provided files. Some users do not know this yet, though, so some additional behavior to detect and warn users who modify the generate files is being proposed.
I am closing this.
Most helpful comment
Relevant core issue: "Avoid re-scaffolding unchanged files (and printing scaffold file information over and over)" https://www.drupal.org/project/drupal/issues/3103090