Suggestion:
make it either so we can select all or de-select all of the objects to choose from or hide
or my personal solution to the problem:
Select show boulders / tree/ bush below each checkbox for this have a button "Select Trees / bushes / boulders" and in this menu there is a select all, select none or the ability to choose. This would cleanup your UI give more control and ultimately reduce clicking, creating the new window is also pretty easy that or just make it a panel of the options window like you have been doing.
Edit:
Also trim the resource names on shift, and replace - with spaces this will be a simple and a start towards properly showin the names of items so it would show "board polar" for example versus all the garbage we dont need, later you can do more string editing to make it so it says Polar board or Polar log ect but that at the very least will save some time, I can even do a pull request for the changes myself if you'd like