But, then, just as if you had booted a real 1.3 rom, wouldn't you lose the HD? It used to be this way, unless newer versions of WHDLoad have a way of "sandboxing" the disk images to run on one ROM, while the rest of your system runs on another?? (I'll admit, I haven't run WHDLoad in quite some time, so maybe newer versions have much better feature sets than previous versions!)
I haven't looked in to it too deeply, but as I understand it, WHDLoad only loads the rom file in to memory. It then uses the patch/relocation info to send rom calls to the one it loaded instead of the rom you booted with.
I don't know how it did it in the past, but it wouldn't make sense for WHDLoad to physically softkick the rom, as that would defeat the purpose of WHDLoad itself, which is to allow you to cleanly exit the game when you're done playing it.