I'll give you my opinion (and it's just that... an opinion
). I think the main reason that it is generally viewed as less-than -desirable to use cross desktop apps is because the inclusion of an app from the "other" side also means that you must build the essential libraries for the desktop also. For example, if you were running a 100% gnome desktop and added Amarock, by adding Amarock you also need to build in the basic kde libraries on top of the equivalent you already have in place for the gnome build.
With respect to using the "other" side apps, from my experience (circa 2005), makes no difference. For example, been using Amarock, k3b etc. in gnome settings with no evil experienced. I also use gnome apps in my current default ops (Mint V KDE).
Again, this is only an opinion... treat it as such