The issue is rather that the failure mode is hard to decipher and debug. Due to fallback and "robustness" of the stack, rather than breaking horribly when things are not where expected, much of this software will shut up and move on, doing it's best to avoid your system being unusable.
However, when you end up with a net result that mostly does not function, you have to get your warning from somewhere, and getting it from the init process is as good as any.
Also, remember that the kind of user who'd put /usr on it's own partition is not likely the user who'd ignore the errors or click through them. It's a user who's technically savvy, has enough knowhow of the oldschool things to commit to such a task, and as such, are well served by this warning.