Grates maybe should be as transparent as floor/wall bars (then again, maybe not to give choice between the two). I personally also enabled it for water wheels, windmills, paved roads and gem and glass windows.
Bridges, depots, wagons, civzones, constructions, farm plots, floodgates, nests, dirt roads, shops, stockpiles, shops and generic windows I left out.
Thing is, any tile using transparency, on top of another tile using an override, will lead to override for the latter not being used (with the exception of natural underlying construction-type tiles, thanks to the fix to items on stairs).
So, even if your tileset doesn't use building transparency for a given building, it will still change game display behaviour if it is enabled for a given building.
So, if you built a bridge over a chasm and arrow lands on top - the arrow will have black background instead of wall/floor tile background.
Or maybe it landed on the windmill you built on grass floor. In this case, it shows the grass floor underneath instead of wall tile.
Or maybe new plants came in on your farm plot. Which would you rather see when it blinks into view, the farm plot tile on your map sheet, or the floor tile underneath?
Or maybe nestboxes, or dirt roads, or etc. are too rare/take whole tile so you don't want to waste additional cycles on them.
Furthermore, glass/ice walls and floors, normally, being transparent is somewhat nonsensical: the transparency displays the tile underneath, but there is nothing underneath a floor or wall.
Also, I noticed for some reason when both transparency and multilevel were on, the empty air floating buildings had their background use chasm/zeroth tile instead of the tile below, such as can be seen on
this POI on dfma. Doesn't happen with multilevel off, though, so...