There's a secret [CURSOR:tileset:tile] command but I don't recommend to use it and probably will remove it because it can replace only the original game cursor, but there's number of plugins that draw their own pseudo cursors with hard-coded 'X' and it's impossible to track and replace all of them. So I'd recommend to use X in the main tileset as a cursor and override it for bins/stairs.
Up/down stairs can be overridden in 4.xx only with an override by tiletype (see readme if didn't use it before).
Leaves are not items, but there are tiletypes for tree parts, so it's possible to override them in 4.xx only. And yes, you'll have to assign different tiles in raws if you want different tiles for different plants (and you can't use numbers >255 of course).
TreeBranches, TreeBranchesSmooth, TreeBranchEW, TreeBranchNE, TreeBranchNEW, TreeBranchNS, TreeBranchNSE, TreeBranchNSEW, TreeBranchNSW, TreeBranchNW, TreeBranchSE, TreeBranchSEW, TreeBranchSW, TreeCapFloor1, TreeCapFloor2, TreeCapFloor3, TreeCapFloor4, TreeCapPillar, TreeCapRamp, TreeCapWallE, TreeCapWallN, TreeCapWallNE, TreeCapWallNW, TreeCapWallS, TreeCapWallSE, TreeCapWallSW, TreeCapWallW, TreeDeadBranches, TreeDeadBranchesSmooth, TreeDeadBranchEW, TreeDeadBranchNE, TreeDeadBranchNEW, TreeDeadBranchNS, TreeDeadBranchNSE, TreeDeadBranchNSEW, TreeDeadBranchNSW, TreeDeadBranchNW, TreeDeadBranchSE, TreeDeadBranchSEW, TreeDeadBranchSW, TreeDeadCapFloor1, TreeDeadCapFloor2, TreeDeadCapFloor3, TreeDeadCapFloor4, TreeDeadCapPillar, TreeDeadCapRamp, TreeDeadCapWallE, TreeDeadCapWallN, TreeDeadCapWallNE, TreeDeadCapWallNW, TreeDeadCapWallS, TreeDeadCapWallSE, TreeDeadCapWallSW, TreeDeadCapWallW, TreeDeadRoots, TreeDeadRootSloping, TreeDeadTrunkBranchE, TreeDeadTrunkBranchN, TreeDeadTrunkBranchS, TreeDeadTrunkBranchW, TreeDeadTrunkE, TreeDeadTrunkEW, TreeDeadTrunkInterior, TreeDeadTrunkN, TreeDeadTrunkNE, TreeDeadTrunkNEW, TreeDeadTrunkNS, TreeDeadTrunkNSE, TreeDeadTrunkNSEW, TreeDeadTrunkNSW, TreeDeadTrunkNW, TreeDeadTrunkPillar, TreeDeadTrunkS, TreeDeadTrunkSE, TreeDeadTrunkSEW, TreeDeadTrunkSloping, TreeDeadTrunkSW, TreeDeadTrunkW, TreeDeadTwigs, TreeRoots, TreeRootSloping, TreeTrunkBranchE, TreeTrunkBranchN, TreeTrunkBranchS, TreeTrunkBranchW, TreeTrunkE, TreeTrunkEW, TreeTrunkInterior, TreeTrunkN, TreeTrunkNE, TreeTrunkNEW, TreeTrunkNS, TreeTrunkNSE, TreeTrunkNSEW, TreeTrunkNSW, TreeTrunkNW, TreeTrunkPillar, TreeTrunkS, TreeTrunkSE, TreeTrunkSEW, TreeTrunkSloping, TreeTrunkSW, TreeTrunkW, TreeTwigs,
In general, I'm not experienced in raws and other modding things, so again I recommend reading the readme from 4.xx version, all three override types are documented there with lists of possible values. Some other override types are planned, but if you have any ideas, feel free to write them. One of the things I do NOT want to do is to deal with materials in twbt.
Ah yes, version 4.57 fixes the crash in automaterial plugin, it was a bug in original plugin that just didn't lead to a crash without twbt.