I have just installed EE 2.9.2 with the latest version of Multisite Manager.
All of my templates are being saved as files
/public
/templates
/default_site
/site2
The template files in site2 however must be manually synced before EE will notice the changes.
Note. Both sites are subdomains. Not sure if this matters.
My config file looks like this:
$config['save_tmpl_files'] = "y";
$config['tmpl_file_basepath'] = $base_path . 'public/templates/';
I also noticed that on site2 EE is not honoring the native template routing. If I want a url to work, I have to manually create a page with the pages module.