Giving WordPress it’s own directory — Did multisite change my .htaccess URL rewrite rules?

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Last year I moved my core wordpress files into a subdirectory. I ended up with a URL change for content assets and the admin.

Such as: example.com/subdirectory/wp-content/…

I just recently I enabled Multisite. Website 2 doesn't have the subdirectory in the URL, but everything still works. I've been trying to understand why. I'm wondering if activating multisite caused the URL rewrite rules in the .htaccess to be overwritten, enabling this new behavior?

This documentation linked below made me realize it is possible to rewrite the URL. However, it's not something that I enabled.
https://developer.wordpress.org/advanced-administration/server/wordpress-in-directory/

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