I totally understand the use case, we are looking at doing the same thing but we don't use SCCM for deploying applications, we use a tool called Scense.
I would say go for it. Create 1 appstack and install the application(s) using SCCM. After creating I'd suggest attaching it to a machine without an Appvolumes agent (attach as Non persistent, if you seal the appstack it is read-only) to check and see what's inthere. I think that this will work. For as far as I can see there is no apparent reason for it not to work.
