I have never used a travel agent for MSC - sailed YC about 6 times. Any small issue has always been satisfactorily resolved. I have no doubt though that like any line there are one-off problems like someone posted earlier.
As to whether “all” the rooms are located within the YC, almost universally true. Some ships have a few suites that have been added as YC to justify a higher cost I presume. These are easily identified during booking. The butler service for these is not quite as personal for obvious reasons. We love them (lots of real estate!) but we are experienced YC cruisers and don’t care any more about escorts to dinner, shows. However you can easily get those by popping down to the concierge desk or arranging ahead of time. (And you will want to do that for escorts off the ship!)
Compared to NCL haven? Let’s just say I will never book a haven room again. If we sail on NCL as we did for a recent Panama Canal cruise, we will book the penthouses that come with butler/concierge service and breakfast/lunch in moderno/Cagneys.