You really underestimate the player base at times. In previous patches the fastest leveling methods were Pulling all mobs up to the first boss in Doma Castle, and spamming floors 50-59 over and over. Still think that latter one might be the case. Havent checked in a while. People are very quick to rationalize best bang for their buck timewise, even if it is excruciating. If spamming 5-10 quests nonstop was horribly boring to do, players would do it if it was the most efficient method.
Problem is this is way easier said then done. We quite literally have 300+ quests in MSQ. Youre essentially saying "Go back and rebalance MSQ rewards so its just a little bit worse than everything else offered, but not so bad that you cant use it to level". As you point out yourself though, people will math things out and find efficiency. If you recieve 10% less exp to do a quest chain in MSQ, but you can complete that guaranteed in the same time a dungeon would take (if not slightly faster) people will do MSQ. Hell, MSQ provides a unique problem with that scenario too. It would not be to hard to set up a bot to do the same quest chain over and over. So you wouldnt have to do anything. Set your bot on at night to do an MSQ where its just run around and talk to NPCs. Whos gonna report you? MSQ is a personal thing, and unlike other bot activities which are more noticeable, this probably will be a lot harder to deal with.
As for PotD, no people still ran in duty finder, but then that was a choice between running a 4 man dungeon in DF and running a 4 man in PotD. Both had the same risk when dealing with other players. Now itd be comparing running a 4 man in a dungeon vs just doing things yourself.
Btw, even if MSQ gave reduced exp, this doesnt solve the initial complaint. Instead of "Why no exp" the argument just shifts to "Why isnt it as good as a dungeon" or "As much exp as MSQ normally?" Considering how vocal certain complaints have been, I am personally skeptical that people wouldnt complain just as hard if the exp values werent comparable to duty finder content. After all, the complaint isnt that NG+ exists, its more about having another avenue to level with. Pretty sure with reduced exp rates, people will consider it a non-optimal method of leveling and deem it a half assed job the devs did and say that this is a worthless feature.