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I think this could gridlock the game. What about clans that have their territory spread out in several places? What about two clans at war with each other but having a neutral clan in between? I'm not saying our system is historical but on the other hand I can't recall from reading about this period that armies on the march were all that restricted by clan borders.
Clans spreading out is a problem in itself. The AI should try harder to consolidate instead they are willing to steal a province on the other side of Japan, and throwing ridiculous amounts of men to protect it.

In one of my Amago games I was able to hold against Toki (they were twice my size) for around a decade before they accepted peace. The AI was willing to travel through half of Japan, taking a lot of attrition to attack me through the straits between Shikoku (since they had some provinces there, I assume they were consolidating forces). In the end they got backstabbed by other eastern clans, because they were willing to commit all their resources to a no gain war on the other side of the realm.

The AI is too opportunistic and risk player.and most of those one province enclaves make it more in danger (from plots and the attention of bigger fish), than stronger.
 
The entire world of gaming treats neutral as impassable.
I don't think you should focus on distant enemies when you will always have at least one potential enemy at the gates.

As of history, I trust alliances also included right of passage but that can only have been for a very limited amount of time and with no looting taking place, hence even allied territory means heavy supply consumption. I doubt we will ever find details of such alliances... we will only find the common enemy and common goals but no other details.
We must assume that locusts passing on neutral territory would definitely cause damage thus altering relations.
 
As of history, I trust alliances also included right of passage but that can only have been for a very limited amount of time and with no looting taking place, hence even allied territory means heavy supply consumption. I doubt we will ever find details of such alliances... we will only find the common enemy and common goals but no other details.
We must assume that locusts passing on neutral territory would definitely cause damage thus altering relations.
I think you misunderstand the nature of pre-WW1 military supply. Supplies for a pre-rapid fire artillery/machinegun army consists almost entirely of a need for food. If an army of 10,000 is marching through a province with a population of 10,000 (a sparse population indeed), then at harvest the population will have 3,650,000 person-days of food. The army will buy (if in friendly or neutral lands) or loot (if in enemy lands) a mere 20,000-50,000 (0.5% to 1.3%) of that food as it passes through with little difficulty.

The only time this becomes a more tricky problem is with sieges. Generally, sieges will require food to be shipped to the army - but even then it will not (necessarily) be from their home base, it will be from the nearest food markets or enemy agricultural land. The Prussian army in the Franco-Prussian war paused before besieging Paris for just this reason - the troops were detailed to harvest the fields around the city and make bread to enable the siege to continue!