Thank you for this report! I already fixed baseOnly, looking into the 2nd.
The 3rd "bug" is intentional because you can't really place saplings on wood, and right now the algorithm only destroys upwards the inital log. This is for realism, although if you want I could also reenable this with a configuration option.
Also you made some very cool suggestions, I'll try to implement as many as possible!
Making drops configurable is a little bit harder though, as I'd either have to manually remove the leaves and then I could spawn the according items. Problem is that I'd basically have to detect the leaves of the tree too, which might lead to the problem that it would destroy the leaves of other trees nearby. But I'll look into it.