Hi,
This can be done. In our 1.0.00 version you can set writable permissions for your .htaccess file and all the changes will done automatically. Don't worry about the same message to rebuild the file. It is rebuilt if you have writable permissions. The message is also fixed in our future version
Well, there are quite few persons who make manual changes in our .htaccess Anyway right now there is no any chance to avoid file modifications
But you can add your instructions in DB so they still exist after each rebuild process. Please make changes in config table - you will see .htaccess lines there