It's not really an odd system at all. Many of the most popular museums in many cities have had to go to timed-entry reservations, even with passes, to manage crowd sizes. The Accademia and Uffizi in Florence, Italy require advance, timed-entry reservations if using the Firenzecard, and The Colosseum and Borghese Gallery (Rome) require the same if using the Roma Pass.
As Barbara said, just a few of the attractions on the Museum Pass mandate timed-entry reservations, and just make a note to start checking availability on others you wish to visit abt. 2 months out. Whether with the pass or not, it's all the same when it comes to reservations.
It's not especially confusing how they calculate usage: it's by hours after first activation. It's easiest not to think about it terms of DAYS but in HOURS. For instance, it you have a 2-day, 48 hour pass, you have 48 consecutive hours to use the card until it expires. So, if you visited your first museum at 10:00 on a Tuesday morning, your pass would run out at 10:00 on Thursday morning. Make sense?
Whether a pass makes economic sense comes down to the math; how much will individual tickets cost if purchased separately? As well, it's possible you'll stop into some smaller museums you wouldn't otherwise visit without the pass. Don't care for what you see? Move on; nothing lost. :O)