Had started my typical EE build (using a bootstrapped config) for a client when they announced they wanted another additional site using the MSM module (le sigh).
So added the MSM module, I commented out the $config['site_url'] and $config['cp_url'] and set those in index.php instead using $assign_to_config.
That's when I discovered this bug where MSM config file settings are not recognized, which is a pain but I can work around it. However, I noticed that when I created the secondary site, it wouldn't recognise my custom location for add-ons and so I had to add that to index.php as well to $assign_to_config['third_party_path'] = "../assets/third_party/";.
Then I discovered that when I create or modify a template file, it won't automatically sync and so I need to manually do that each time which is a real PITA.
Why would my templates not be syncing to the database? Is this related to the MSM config bug?
While I haven't tried bootstrapping the third party path yet, I've definitely been able to bootstrap the template path for MSM sites... What bootstrap method are you using?
Are your sites on subdomains or subfolders? I've only had experience with subfolders so perhaps that makes a difference (although it shouldn't).
Could you maybe walk through in a bit more detail what's happening? Your first site (site_id = 1) templates sync automatically from filesystem edits, but your second site does not? Yet if you go to CP > Design > Synchronize Templates, that works?
The $assign_to_config portion of MSM setup is definitely a weakspot when it comes to bootstrapping... I wonder if we need to work up an additional bootstrap for MSM+CP environment, where it looks at the cp cookie ($_COOKIE['exp_cp_last_site_id']), and sets values based on that.