How to use edited inventory file?
You have this in your config file:

[inventory]
enable_plugins = host_list, script, auto, yaml, ini, toml


Do you really need all these plugins?  If not, they'll just add time to your processing.  There is also a small chance that one of them is successfully parsing your inventory file as an empty inventory.  And the documentation states that


  Once an inventory plugin succeeds at parsing a source, any remaining inventory plugins will be skipped for that source.


If you do not need those plugins, I'd comment that line (or rework it to remove some of the items).

Also, are you sure that it is using the local hosts.ini?  The command ansible-config might help confirming that.

Regarding your first question ("Why I have empty hosts.ini in my execute directory"), there is nothing in your playbooks pointing to that file being created or modified.  Did you mean to  have it modified?  Or you don't know how it was created?  The question there is not clear.