no, this does not affect backups or file storage.
It is the config file that gets two entries for each domain, one for http and one for https, with the information about what filepath to serve files from, mainly due to the ability to keep http and https separate with using private_html for the https content (you can set a symbolic link to use the public_html content for both). This is probably not a huge issue for most shared hosting setups but with free we are a bit above average with number of accounts per server (which is why it is a bit restricted compared to our paid plans).
As for issues editing records it could definitely be related to the double data in configs. Though when I just tested on my account that happens to be on x11, it went through rather quickly when I changed the IP of a subdomain.