With Transform, when I use scale I now get an area of the image where I can clone in blank space. Effectively there is a layer and that can't be cloned into in LR. Is it possible to "flatten the image to permit this?
Please post a screen shot of what you are seeing.
I've yet to use that feature myself but IIRC there is an option, a Check Box, to do what you want Automatically. Other than using that option I don't think LR can do what you want.
And at this time I am not running the latest version of LR because of a bug in the ACR section that doesn't read Fuji RAW files converted to DNG files. So I had to Roll Back to LR CC 2015.5.1