Isometric: different graphical tile size from level cell size

Hello! It’s the first time I’m using tiled for a project, and I’m not sure if I’m doing something wrong or if this is not a use case tiled can support.

In my isometric engine the game logic is using a 64x32 “level cell”, but each cell is made up of 4 32x16 graphical tiles. Right now I’m using a 32x16 tileset in tiled, and I can associate them with level cells in my loading routine no problem, but this is sloppy and leads to lots of mistakes during map building, with odd tiles that half-cover the next cell, or mis-aligned tiles and so on, that I need to constantly be at the lookout for and fix.

Is there a way to have a 32x16 tileset but have tiled only allow me to place them in 64x32 super-tiles on the level, or something else that would work with my setup that I might not have thought about? Is there a way to support such a setup?