We've also hit this same issue (wanting to use NavmeshCut to modify multiple recast graphs that we are using to support different sized creatures). Did the branch mentioned above that supports setting which recast graph to use in TileHandlerHelper ever make it into the main code base? If not, would it be possible to get a copy of the code?
If I was going to do this myself, I was thinking of just removing the check that destroys multiple TileHandlerHelpers and then adding a field that lets you select which graph to update. Then we'd just have multiple helpers each updating a different graph. Is this the best approach?
Additionally, to support the case we're talking about here, it would be great if the NavmeshCut script supported getting the character radius from the target graph and factoring that into the cut so that different sized characters could avoid objects more accurately. Right now I'm assuming we'll just have to set the cut sizes to accommodate the largest possible character, meaning that smaller characters will avoid the objects more carefully than they really need to.
Thanks for any help!