I got "RewriteBase: only valid in per-directory config files" message when I tried to change some redirect on my hosting.
Turns out that if I move the redirect section above the part added by wordpress, both my redirect and permalink will work...
For example, I wanted my domain to add a redirect to my wordpres console, I move the section that wordpress written to the bottom of my .htaccess:
RewriteEngine on
RewriteCond %{HTTP_HOST} ^mydomain.com$ [OR]
RewriteCond %{HTTP_HOST} ^www.mydomain.com$
RewriteRule ^mywordpress$ http://www.mydomain.com/wp-login.php [R=301,L]
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress