Carrot Cruncher on "[Plugin: W3 Total Cache] W3TC for WP in a subdirectory, which .htaccess?"

Hi. Apologies if this has been asked before, I've searched and searched but can't find an answer. I have WP installed in a subdirectory as per:
https://codex.wordpress.org/Giving_WordPress_Its_Own_Directory
All the other WP plugins I have installed amend the .htaccess file in the WP subdirectory but when I active the W3TC plugin it amends the .htaccess file in the root folder. Is this correct? Won't these settings filter down to the non WP subdirectories? Cheers.

https://wordpress.org/plugins/w3-total-cache/