-If you overlap the ways on top of each other without using relations, you won't be able to tell how many ways are on top of each other.-
yes you can if using JOSM. user shouldn't be messing around with mulitpolygon relations in iD anyways. 
more difficult to change is an understatement. 

There are many shared landuse boundaries not using multipolygons without issues, thus avoiding overcomplication (whenever we can get away with it). that's how I approach this kind of mapping. 