The chopper uses one set of input slots for both tools (axe) and saplings. When trying to automate these with AE2 I can't find a way to limit how many axes or how many stacks of saplings, and invariably the chopper fills up with four axes or four stacks of saplings and the farm breaks.

It would be nice if the chopper would have separate input slots for tools and saplings, or some way to lock input slots according to current inventory, so that any dumb "insert objects" (like a hopper) wouldn't break it by overfilling the inputs.

Currently I have a "solution" in dev which is just to never plant the last sapling on a slot which I think is enough to solve this issue, let me know if you'd prefer a different solution. And sorry for the delay in the response

That should solve the four-axes problem, but not the four-stacks-of-saplings problem.
FYI I came up with an alternate solution for my case - I used two choppers. One only has saplings, the other only has axes. I put them beside each other and together they tend one area.

If the "never plant the last sapling" were combined with "and never put a sapling in a slot without saplings" that would effectively segregate the slots into sapling slots and not-sapling slots. The user would have to pre-fill each slot with a sapling, or leave empty for axes.

Hmm yeah that's a good point, I'll probably do that and split the slots in: 1 for axes, 1 for bone meals and 2 for saplings. Does that sound good? This would also allow to add an "empty slot sprite" for the background which I really like the way they look :P

That would work too. Thanks!

Implemented as of 1.7.0