Yeah, I have separate M4 and V4 runtimes. So long as any additional morph packs (like the Morphs++, creatures, muscles, A4 and G4 for example) get installed to the V4 runtime and V4 is initialised, it runs hunky dory. Same with M4 stuff (morphs++, H4).
The only problem I had was when I tried something out using P6 and forget about the separate runtimes. Then M4 and V4 took about 15 minutes to load!  :)