Don't create config files for flags_lists

I manage thousands of per users flag_lists (5000+ flaglists for 2000+ active users)
i consider thoses flaglists as content, not as configuration
the flag_list template only is a configuration

is there any way to disable config files generated by flaglists made from a certain template ?

i already use config_ignore module, but i am not satisfied with this workaround

[edit]
Flags are by choice config entities, so i imagine there is nothing i can do against that. It's logical in a pure flag point of view, on the other hand in the flag_lists point of view it's not so obvious.