As the person who built amarok-1.4.5, I chose to use the system sqlite rather than the included one, simply because I didn't think it necessary to add extra bloat by using the included sqlite. It's also entirely possible that an older, more vulnerable version of sqlite is included with amarok.
All valid reasons. Just going by amarok's website, they suggest that the included sqlite3 will speed up amarok, because it is statically linked to the amarok binary. In addition, one of the changes in 1.4.6 was the update of the included sqlite. On the other hand, I suppose if several of a user's programs use sqlite, one wouldn't want to duplicate it. And if a new version of sqlite is released it would be preferable to upgrade it, without having to wait for a new amarok release. (They also suggest that for large music collections, one would be better off compiling it with support for mysql).
Of course, a packager cannot try and squeeze in all the options that will fit everybody's taste... If someone wants to try different compiling options, they can always get the source. As for me, I think you guys are doing a great job with the repos, and I'm happy getting it from gslapt.