I’ve been looking for details on why that line is suggested for a multisite install using subdomains as well. I actually question if both of these are relevant for a subdomain install:
RewriteRule ^(wp-(content|admin|includes).*) $1 [L]
RewriteRule ^(.*\.php)$ $1 [L]
In a sub-directory install the rules are setup slightly different to strip the sub-directory name from the request to be something like:
RewriteRule ^([_0-9a-zA-Z-]+/)?(wp-(content|admin|includes).*) $2 [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(.*\.php)$ $2 [L]
I’m seeing a redirect loop in my error logs and it’s caused by the first version of these rules since the replacement text is identical to the original text. I found some evidence that some versions of mod_rewrite will detect that the original and new text are the same and skip the re-insertion of the result. (Not sure which of the many links I’ve been reading at this point.)
I see no value in rewriting a URI to be identical to original and thus causing the link to be reinserted into the rewrite engine. With the rules removed I get the expected 404 page instead of a redirection loop that ends in a 500 server error when the redirection limit is exceeded.
Separate note, I think that the suggested sub-directory version is also broken. Because it uses ? for the sub-directory portion, it will loop on an input URL like no-such-file.php. Matching on the sub-directory portion should not allow for zero copies so the rule should likely be:
RewriteRule ^[_0-9a-zA-Z-]+/(wp-(content|admin|includes).*) $1 [L]
RewriteRule ^[_0-9a-zA-Z-]+/(.*\.php)$ $1 [L]
A similar conclusion is found here: https://wordpress.stackexchange.com/a/73185/27576