According to NYT, Ds are only supposed to win about 7% of PV but are getting a majority of 23.
I read somewhere that this may be because they are not counting any votes in the races that are uncontested as Dem votes.
I haven't verified that this is the case, but that is something that should be checked after all the dust settles.
While it is true that counting the votes in those races would overstate the "true" Dem popular vote in the sense of reflecting the will of the voters, not counting them also understates the "true" Dem popular vote.
For a proper estimate of the "true" popular vote, you would have to plug in a rough estimate of what Republicans would have gotten in all the races that were unopposed, if they had candidates there (and likewise for Dems in the 3 or so seats without a Dem candidate).