Oh man, I swear I'd read somewhere that there was some advantage to having them push through instead of sit on top, but hell if I can remember now. And ain't that a bitch, the process to change that around is going to suck. It does make sense though, it always seemed odd to me that once I had the car up on jacks, I couldn't turn the wheels because it would get caught in between the flanges of the control arms. Which also makes sense why I would hear bad sounds over bumps or into dips (especially the latter). So yeah, that sounds like a solution in the works.
And yes, all bushings were changed - I'd be a fool not to with the entire front end all apart!