Yes, you can.
But to answer your question more precisely, in the density tab, by default,  dacay near foreign object is checked. And your tree is a foreign object, so the density is adjusted to leave 5% space around your tree.
You can change this behaviour by unchecking the decay box, but there will be absolutely no dacay near ANY object, which you may want or not, or, in the aspect tab of the object manager ( under the preview sphere), with your tree selected, click the tiny icon taht looks like a branch. This icon means Ignore this object for ecosystem population. So this tree will no longer be an obstacle to populate ecosystems, but any other object you want decay  around it will still be able to do it.