If you're planning to do it the old-fashioned way & stuff them individually, they'll just take longer to stuff. If you plan to do it the modern "faux-trapunto" way by adding an extra layer of batting and trimming away, my only concern is whether there is enough space around/between the trees for you to do your microfill stitching.
The second issue is that if you plan to wash it on a regular basis, the far apart quilting lines will put a lot of stress on the applique fabric; it may wear out faster or have the stitches anchoring it to the quilt snap from the stress on it whenever the quilt is pulled, sat on, laundered, etc. I would at least stitch around the door & window to provide enough support for the applique pieces.