The thing is, the system doesn’t know that your alt has a rank 3 essence that your main doesn’t until you log onto that alt. It’s exactly the same as it was with account wide transmog. Log in to all your characters you want to participate in the system with first so the game knows about all the stuff you have and then resume business as usual.
The more glaring issue is, how much this screws over people who main DPS class (who are imho much more likely to roll a support class alt). I’m lucky enough I mained healer for a bit in S3, so apart from the new healing essences I got pretty much everything across my characters, but if I had just my warrior, I’d be back on the “no alts” boat, because I want a healer alt.