Since most of these are new things, i am not sure if some are intentional:
1. The models of the of the Proto Gun used by Cool-Knight and the Proto Sword of Regal-Knight use the green Proto skins instead of the copper-like one, which is used by the Proto Shields and the Proto Bomb and is also shown for them in the picture in the Spiral Uplink.
2. The name of the seemingly Strangers is for all three of them shown as Keepoh, if you look at them, but when talked to they show the names Botshoes, Kneepo and Wargel. (This is in the German version, i don't know if it is the same in other languages.)
3. The damage chains of those three energy balls/bullets (Is there an official name for those?) rotate faster than their machine attached to the wall
4. NPC-Knights are able to target invisible Ghostmane Stalker.