Ставьте редиректы сразу после // RewriteEngine On
Например:
RewriteEngine On
RewriteCond %{HTTP_HOST} ^www\.(.*)$
RewriteRule ^(.*)$ https://%1/$1 [L,R=301]
RewriteCond %{REQUEST_URI} !\?
RewriteCond %{REQUEST_URI} !\&
RewriteCond %{REQUEST_URI} !\=
RewriteCond %{REQUEST_URI} !\.
RewriteCond %{REQUEST_URI} ![^\/]$
RewriteRule ^(.*)\/$ /$1 [R=301,L]
RewriteCond %{HTTPS} !=on
RewriteRule ^(.*)$ https://%{HTTP_HOST}/$1 [R=301,L]
# RewriteCond %{REQUEST_URI} /index.php
# RewriteRule ^(.*)$ https://domain.com/ [R=301,L]
