You are free to edit the DocType in your layout.master file. You can change it as specified in the facebook documentation or in the stackoverflow post you linked.
mojoPortal won't care about the doctype. It may affect validation according to the w3c validator but its not going to cause any problem in mojoPortal functioning.
Some of the skins we ship use Xhtml doctype and others use Html 5 doctype, but you can use whatever you like.
Hope that helps,