It’s a historical fact that she won something that neither candidate was aiming for. You can’t just assume that the popular vote winner when neither candidate was concerned about winning the popular vote would also win the popular vote when both candidates were trying to win it.
Hundreds of millions of dollars are spent on campaigning. Countless thousands of campaign workers help support their candidate. Currently these resources are deployed for the specific purpose of winning the Electoral College vote. If the objective was to win the popular vote then all of that money and manpower would be deployed very differently. There’s simply no way to know what the outcome would have been.
I think it's incredibly silly to think that the Clinton campaign wasn't interested in winning a plurality of votes. The idea that any campaign doesn't care if they relate to the majority of Americans(all of which that they will govern) is about as stark of an example of a naked power grab as I've ever seen.