I just started with this mod, so I may be doing something incorrectly.

When I placed the smelter, it takes the 25x25 space, but is represented by a normal sized radar in the middle.

Well, there are both. There's the 25x25 smelter model and then there's the radar in the middle. The radar is there because when you have stupidly large buildings (250x250+) it actually lags the game out really bad to not have the radar there. Radar gets to do a parallel and cheap map update path, but not the other forms of map update are all single threaded and not cheap. So the radar is 100% a performance boost, on top of being a QoL feature. I could probably do some tweaking and get the radar to render on a layer below the smelter, so you couldn't see it, but meh.

I'm not seeing the smelter model, just the normal sized radar.
The "footprint" still shows the 25x25 area.

Hm. that's gotta be a mod conflict, but I don't know what a mod would be doing that would modify the drawing box of random entities. That makes no sense to me.

Even when I just use your two mods (smelter and assembler upsgrade), it still is a radar. The size of the smelter is 165*165 if that has got anything to do with it.