When "Stretch/Upscale" is off and "High quality" mode is off every output file should be resized to 1080x1440.
But when original image is smaller than 1080x1440 it should not upscale entire image - just add blank margins.
And my tests shows that work correctly.
Original image (800x1200):
http://i.imgur.com/3DpIYuK.png
Output (1080x1440):
http://i.imgur.com/4HcWJC0.jpg
Output with enabled upscale (1080x1440):
http://i.imgur.com/v46ODe5.jpg
So I don't really see your problem. Yes - images are placed on bigger canvas but are
not upscaled.
Denoise - Not planning too. This program is created to convert files that have perfect quality :-)