I have the same problems as well with the OS X client. It definitely has issues handling external drives. It somehow doesn't display my exclusions of files on external drives anymore, but somehow is still following them.
I'm really happy with their service (had it for ~2 years now), but would love to have a tool similar to how you describe with reduced bugginess and more tweaking ability.
To follow up on this, it actually turns out the configuration for backblaze on OS X is in XML and tweakable. It can be found in /Library/Backblaze.bzpkg/bzdata/bzinfo.xml
I'm really happy with their service (had it for ~2 years now), but would love to have a tool similar to how you describe with reduced bugginess and more tweaking ability.