This is not the main difference (which is that apt packages are checked by package maintainers), but thanks for sharing the link, didn't know that. It makes this hack even more serious.
There's a world of difference, as long as you are using only default repositories (which you should). Apt itself is root, of course, but it is (or should be) trustworthy. All other apps never see root access unless they need it - and if it is needed, then the package maintainer has checked the package to make sure it only uses root when necessary. Kind of like Apple checking apps on AppStore.
Not sure if this is how they do it, but OS X has another option (which is in fact recommended by Apple for all tasks needing elevated permissions): installation of a privileged helper tool.[1] The helper tool communicates with the main app via IPC, ideally such that the only things the app can ask are precisely the things it's supposed to do (e.g. the helper will only sneak in accessibility for the dropbox app, and nobody else). The helper tool removes a lot of the surface area for security holes, assuming the IPC protocol is well written (not something like "here's this string, run it as a shell command with root privileges).