TL;DR
You shouldn't be able to build/claim inside an enemy guild's claimed territory, if you want to build there siege it and claim it for yourself.
Overlapping territories makes TC a meaningless, goofy and bad player experience.
House and SH claimstone territories should behave as a TC claim/build exclusion zone to non-allied players so enemies can't just plop houses with claimstones in the middle of your supposed "territory" and have overlapping territory claims allowing them to build "territory control" structures inside your "territory" while you sleep.
If you want to claim an area you should first have to siege any enemy buildings there containing a claim stone, removing their territory claim and allowing you to build your own house/SH with a claim stone, claiming the area for yourself and preventing enemies from being able to simply rebuild in the same spot while you're asleep.
This will make TC actually meaningful since it will become worthwhile for guilds to siege each other's assets (despite the high cost to siege) in prime locations to claim it for themselves and deny it from their enemies, with their own territory claim being protected by the high cost to siege if their enemies want to reclaim it.
We can keep the high cost to siege so random bluebob villages who mind their own business and are situated out of the way don't ever really have to worry about being sieged. The only players/guilds that sieging would be a concern for are those who are trying to compete for highly contested areas.
The radius of the exclusion zone can be tweaked and balanced, but I think anywhere from 20m-100m would be a good starting point. Note that I'm saying this should only exclude TC claimstones/buildings. It should not prevent building houses, just prevent putting a claim stone in them or building TC assets if it's near a non-allied TC claimstone/asset.
What about existing overlapping territories or when a guild drops alliance with territories overlapping their former allies?
Simple solution: Put overlapping territories in a "conflict" state where all TC functions of both zones are disabled (no guards or TC NPCs) until the conflict is resolved through one of the opposing claims being sieged/removed/decayed.
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