Look at this image and tell me where the Calculate node (brown tint) input wires come from (it is currently selected). I find it very hard to trace cables sometimes. Having the ports half hung-off the nodes makes no difference IMHO, even in the example comps I notice cases where wires are overlapping and impossible to trace. (Tracing wires was the original rationale for port position relative to node edge in Vuo pre-launch days).
Now consider this possibility. Wires get colours assigned in order of input ports no matter how many nodes are selected, all node input ports get coloured in this way until deselected.