In order to answer your question accurately, it would take a considerable amount of research time in the manuals.
So let's talk about a couple of obvious differences.
When the 200/400 models were released in 1969, the rear PTO valve was not at the rear. Just the lines were. The valve itself was mounted on a metal bracket that bolted to the side of the Kohler engine and steel lines when from that valve to the rear of the tractor.
When Case added 2 inches to the wheelbase of the 400 Series, that called for a different set of lines from the ones used earlier on the 200 Series and short wheelbase 400's. It is also conceivable that Case tried more than one way to route the lines for reasons known only to them. Case purchased hydraulic pumps, motors and valves from several different companies over the years. It may be that a change in valve supplier created a need for slightly different lines.
As I said to you once before, it is a good idea to record the PIN and model # of the tractor that PTO kits, Holding Valve kits and Flow Valve kits are removed from and tag all the parts. That way, you know for sure what tractors that kit will fit with no modifications or headaches.