I don’t know what behavior to expect when bringing a sub tool from R6 into R7 will have but I would imagine it would transparent.
On other hand, what I am about to say is based on my observation and when I have been using zModeler/QMesh…
You can use zModeler Brush tools on a mesh not initialized using the R7 Initialize, the problem is such meshes tend to be too numerous in polygons to be of any effective use. The reason for this is because when you use R7 initialize you start out with a very low polycount that allows you shape your model and in tandem using dynamic sub division to get the desired overall shape and tone. The two tools are two peas in a pod so to speak.
In my opinion its not practical to use zModeler on large polycount meshes as I understand it based on my own experience, which I will be the first to say is limited and not enough. Someone out there may be doing something extraordinary but I have yet encounter it myself. The reason for my opinion, is that zModeler tools rely on an action, a target of polygon(s) and any modifiers. Applied to a large amount of poly’s like thousands or more, it will do what it does but the outcome would be “mirco” compared to using on R7 initialized cube.
As far as the undesirable wrinkle effect I would imagine it would depend upon what your target settings are:
For example:
A single poly only impacts that one poly.
A polyloop impacts all polys in a complete row regardless of polygroups
A Flat Island is going to impact an entire surface were the polys are adjacently flat to either other regardless of polygroup
Its possible that you are dealing with so many polygons your pen tool could be hovering over an edge or a point instead of a surface. With so many polygons its almost unpredictable to realize the outcome of action and target in my opinion.
Not sure if I was of any help, but it may be something ponder on