Ok, checked out your new version and it works great. There are no trees overlapping others from above so mission accomplished on that score.

However, I know you said it's a little buggy but I noticed one thing you might not be aware of. The only way I could get anything to save from it was to overwrite another file. It won't save an image if I give it a name such as "Treetest.png" unless that file already exists. Not a huge problem I guess now I've worked out how to get around it but I guess something you want to fix.

Another thing I noticed that you might want to adjust is when you click the "fill" checkbox it redraws the whole image randomly again. I know that this is how you've intended it but if you can somehow make it so that clicking the "fill" checkbox just leaves the same image but with a masking background that would be awesome.
The layer WITHOUT the background is good because you can do more with it as far as blend modes go. However, if you wanted to paint a colour behind it it is awkward because of the transparency of the image. Having another version of the same image that you can use as a mask, the filled layer, would be great for manipulating whatever layers you want to under your elements. I say again, that would be awesome.

LOVING your work on this by the way and I'm REALLY looking forward to you refining this further. I know that I for one will be using this tool as I'm sure will a lot of others. I'll rep you again as soon as I can.