When site is replicated RewriteBase in .htaccess stays the same which breaks sef urls (articles load from template site instead of slave site)

Well, here is the patch

Sorry but JMS can NOT touch the standard htaccess files.

I don't see the reason why to have to change the Rewrite base if you have correctly setup your hosting server.
Normally the rewrite base is "/" and I don't see the reason why you want to change that with the domain name.
Just assign correctly your hosting server with the appropriate document root directory and the "/" rules will be OK.

In addition, the quick review I did on the code you provided to mean seems only applicable for IIS platform and probably will not work correctly on unix platform or windows + apaches.

that code was developed for and successfully tested on linux/apache
Rewrite base is necessary when joomla folder (i.e. index.php) is not located in root folder of web server for sef urls to function properly - you can read about it in documentation of seo plugins

Give the url where we can find the diocumentation of the specific seo plugin you are using.

If you have a look in your code you will see that you are using SCRIPT_NAME that is variable only present for IIS.

I got it from my phpinfo()
It's redhat system with apache - no doubt about it, i'm sshing it.

Here: "404 Page not found" error after clicking any link

Finally, make sure to set the RewriteBase value to match the root URL of your Joomla! installation at the server.