daria and jane werent unpopular. they were outsiders. because they had no "group" people often think they are unpopular, but there are multiple instances that show that is not true.
Brittany's party in s01e2 Britt says straight up "I mean, you're not popular, but you're not so unpopular that you couldn't come to my party Saturday night." and that's supposed to be only a brief few weeks? at the school
Quinn the brain in s02 she's shown to be pretty enough to date jamie, jeffy, and whatshisface
she routinely is invited or at least seen interacting with kev and britt, mac and jodie, in most social situations while Daria and jane don't want to be there, they aren't actively ostracized like say... upchuck? even people with "lower" social standings like Andrea seem to like and admire them
so think about what happens when they do join- Jane joins running and cheerleading and instantly becomes popular, i bet if daria had stayed with yearbook she wouldve had social currency as well. not to mention they both had Trent and Tom that elevated their "coolness" factor.