I did MSQ with one job, all MSQ quests and dungeons but no side quests. I came up a tiny bit short of (I think) level 87 in the fifth zone and maybe 10% short of level 89. If the aether current sidequests were factored into the "correct amount" of EXP then that would explain it.

For everything else, I had no issues, and once I did get up to level 89 I got exactly the right amount of EXP from the MSQ to hit level 90 on the second-last level 89 quest.

Since then, they've announced that they've buffed the EXP gain from dungeons, so nobody should have any issue as long as they're playing with a single class.