The original Monorails were indeed the same level as the platform, or maybe 1 inch higher....
When the "new Delta Monorails" were made to replace the original Monorails, it was a fast decision based upon the Monorail fire which burned car # 6 of Monorail Silver, down the the frame right on the Epcot rail.
The construction of the new Monorails was contracted out for as quick a replacement as possible for the old Monorail system.
In effort to increase Monorail capacity, Disney considered having the new Monorails made with limited seating, and added standing room.
Disney surveyed guests waiting in line for the Monorail, asking them if they would rather wait for the Monorail and have a seat, or if they would rather wait half of the time, and stand on the Monorail...
Commonsense dictates that if you are going to stand in line anyway, then you might as well stand in line less time, and stand on the Monorail... you are standing anyway!
So the new Monorails were designed with 1/2 the amount of seats,and room for standing guest which would almost double the Monorail Guest capacity.
To create standing room on the Monorail, the Monorail had to be larger in height, and the doors would automatically open and close using a similar system as those doors on the Buses.
The door system requires a glide hinge on both the top and bottom of the door of the Monorail, and this makes it impossible for the platform to be at the same height as that of the Monorail guest rider's floor unless there would be a large gap between the Monorail and the platform, creating an unsafe area for a foot to fail between the Monorail and the platform.
In addition, the Monorails now being larger and taller, had to run on a track designed for the old Monorails; Stations and access to the stations were all designed for a certain size Monorail, and when the new Monorails started service, they did not fit the access openings requiring the continued use of the old Monorails until the roofs were raised and the access openings were widened.
Disney had to close 1 Monorail track at a time for months as these alterations were made, to allow for the use of the new Monorails
The twist to this story is that the new Monorails do not really carry more guests then the Original Monorails did, because people simply do not pile in to the standing area as Disney thought that they would.
A very tiny amount of time was saved with loading and unloading, and all the efforts resulted in the same wait times... only now, 1/2 of the guests had to stand.
Now, with the Automatic Pilot driver-less system upgrade to the Delta Monorails, wait times are even longer, because the Auto Pilot drives the Monorails slower, and with jerky responses.
Wait times are largely based upon how many monorails are on the rail at the time.