How to handle overrides?

As soon as I move any link in the assigned menu, I get a config override in core.menu.static_menu_link_overrides file. Then after clearing the caches the menu items get reset to original weights.

In my case I need taxonomy terms in the main menu along with other pages, so when a new term is created it goes into main menu root automatically, where it can be moved below any other menu item. But now after a deploy all config is imported automatically, which means all the term menu items come back to the root of the main menu.
Should I exclude the config file core.menu.static_menu_link_overrides.yml from code repository to prevent it from being reverted? Doesn't sound like a good solution.