it's fine to do that with it, and i'm sure it sounds great, but in the markbass little mark amps (which your combo head is), you can't defeat the markbass preamp by sticking the vt in the return. the loop is positioned before the pre.I have never noticed any 'clanking' associated with the VT Bass - just big, warm, tube amp like tones a'la Ampeg. The VT Bass Deluxe straight into the effects return of my MarkBass Jeff Berlin 1x15 combo is IT!!! Clank-free too.
however, the little marks have near flat response with all controls at noon and all filters off, so you could run it anywhere and still achieve what you're looking for by trying to defeat the markbass pre.