Lightroom offers direct control of file and folder locations through its UI, unlike Aperture, and both offer virtual folders, Lightroom's being optional and Aperture's compulsory.
OK, I see where you're coming from.
And yes, Aperture (stemming from it's inception) has assumed that you don't care where, exactly, the original image files are stored on your drive. For lots of folks, like me, that works fine - let the computer keep track of such things as long as I can find any output (JPGs) I might produce. After all, I can create books, order prints, create slideshows, make prints and even email JPGs without having to touch those files. Others want the ability to "see" their files out there on the hard drive; and they really hate Aperture's managed system.
But that managed system allows for Aperture's ability to save vaults as all inclusive backups. Lightroom users depend on other backup systems.
The "consolidate masters" command is for moving originals back into Aperture's package. But if you do want to move referenced files around on the drive, you need the "relocate masters" command.
In the end, as I've often said, the Aperture vs. Lightroom discussion has a lot in common with the Nikon vs. Canon discussion. Both are powerful and effective tools about which intelligent people can disagree on which is "best," because a lot comes down to personal taste.