Wow, that took way longer than I thought it would to debug. I'm not entirely sure why it wasn't broken before, because the actual numbers being used for the scaling logic haven't changed from 9.2.x to 9.3.x, but it seems the Foundry apparently has squeak through functionality built in?
What I mean by that is, the collision box is smaller than its selection box in vanilla, allowing the player to walk through them when they are placed directly adjacent to each other. This is unlike the other 5x5 entities (oil refinery and cryogenic plant), which have identical collision and selection boxes.
At some point in the past, I made it default that all mini machines would have squeak through rescaling built in, making their collision smaller than their selection, but since the foundry collision was already smaller, this squeak through rescaling stacked on top and made it so small that it fell into the 2x2 entity size. Disabling the squeak though effect fixes things, but unfortunately doesn't allow the player to pass through anymore (annoying math things)
And since I foolishly hardcoded that squeak through rescaling value in stdlib (which I don't want to update for such a minor thing), the mini foundry will have to live without squeak through functionality for the moment. Quite the annoying little bug, but I consider it a minor cosmetic issue for the moment.
Anyways, tl;dr should be fixed in v9.3.6
