rewrite rules always flushed

It seems you forgot to change a few parts regarding the custom post types as they always call flush_rewrite_rules() which uses $hard = true as default value and always overwrites the .htaccess file.

See also https://developer.wordpress.org/reference/functions/flush_rewrite_rules/

I have applied the following changes to resolve this:
https://gist.github.com/DanielRuf/c894deae0b904750b860f8bdb38c452e/revisions#diff-dc12a7c005d7301b56f3e7b2a1bcbb41d951f2b66a4c46a59abdfe167fba92a7

You might want to refactor this part and check if at least one custom post type is created and only then flush the .htaccess file but only once.