But is it a long side quest? Is it worth going through Blackreach twice, or wait til I get the Elder Knowledge MQ and do that and Discerning the Transmundane side quest at the same time/
You won't have to go twice. Both the MQ and Discerning Transmundane require you to find the Elder Scroll of Blackreach, but the same Elder Scroll works for both quests. Neither quest consumes the Elder Scroll, so no need for a second trip.
Spoiler Though after the MQ, you can hand the scroll off to the librarian at the College of Winterhold, so I'd make sure I was done with it before then.