Sorry, your information is not correct, on two accounts. First of all many people keep data on their desktops, whether it is good to do so or not. Since the desktop is included in the User folder now and so should be backed up with everything else in the folder it should be no problem. I myself have about 50 gig. on my desktop.
Secondly, I have been building computers for a while now with an SSD OS drive and a data SATA drive and I do include the 'desktop' folder on the SATA drive using the method you outline. I have never had a problem. I have it that way on my computer as well.
Just thought you might like to know .