I don't believe you. Apple includes OS standard versions of packages like SQLite and Python, are you of the opinion that developers shouldn't use them?

If they are standard and public and they work, sure. If they're not public and not standard (like MacRuby) then probably not.

I think the GP post was simply referring to the fact that a vast majority of software is 'installed' on the mac. Just drag it to the application folder. And drag it to the trash to uninstall. This almost certainly means you have a bunch of duplicated library files on your computer, but also means each app doesn't have any external dependencies.

I know Firefox bundles its own sqlite on OS X because the native sqlite is far too buggy.

For a long time (maybe even today), the system sqlite3 did a full filesystem sync every time you did an UPDATE.

As is required to make sure that there is no data loss. Yes, it is a performance loss as well, but it makes it much better with regard to possible crash scenarios.