I just ran an instanced MSR with a tank. I asked someone on the team to track their VMs earned and the raid leader, Psyheal, graciously volunteered to provide me their beginning and end number. Psyheal assured me that they spend their raid time in the bowl. I made sure to spend at least 80% of my time out of the bowl, fetching Rikti.
The results:
Beginning
End
Raid Total
Me
69
1181
1112
PsyHeal
17
1138
1121
There's a discrepancy of 9 Vanguard Merits that I can't account for. A trivial amount but it does annoy me. My hypothesis is that it's related to pylons, I got distracted early and missed on some pylon kills but this is irrelevant to the greater point that pullers are not penalized for spending time outside of the bowl for instanced MSRs