The squares on the space bar do look look smaller but are actually ~3mm just as they are on the round buttons.
The F12 button is rotated because the bridge distance was a touch too far which made the bridges kind of weak in the middle. I had the same issue with the escape key and directional pad. I handled them as delicately as possible during assembly so I only broke the two bridges. It is a fine balance from a design perspective, too many layers and it won't be flexible too little and there is not enough strength. I think the model is pretty close to right. If I tweaked my settings a bit more I could probably get a slightly more robust bridge.
As for the clips the ones around the screen bezel fit perfectly but did not have "retaining" power, meaning they were easily un-clipped from the bottom shell. This simply could be the material (PLA) warping due to thinness of the print in this area. So I am not sure anything could be done to make that better. Maybe slightly angling the clips in towards the bottom shell?
The bottom clip had maybe a half a mm of play where it clips to the PCB. This caused the bottom keys to raise the face plate slightly when pressed which gave the keys a different feel (a lot more travel). By heating that up and curling the tab over I took that play out.
The tolerance between the buttons and the holes in the face plate is perfect. The alignment of the face plate buttons to the underlying dome switches on the pCHIP are also perfect. The outline of the LCD and fit around the bezel (including the flat flex for the digitizer) is perfect. The alignment of the top shell to the bottom shell is also perfect.
I would say overall it is quite a good fit and well designed for 3D printing.
If your interested in any close up pictures or seeing how the keysforbuttons print up let me know.