I know Square and Enix merged back in 2003, but should there be an enix company tag for games they produced before the merger? The wiki will list the games to avoid confusion.

There is exactly such a tag already in existence.
It isn't heavily populated, but it does exist.

Don't use it for anything but crossovers though.

Sounds good.

Log said:
Don't use it for anything but crossovers though.

...and always in combination with the company_connection tag for those crossovers too.

Isn't company_connection for multiple depicted series from the same company?