Submit an enhancement request. I've run into at least one other major shortcoming of Variable Patterns - lack of support for Hole Wizard features. I'm guessing they'll fix that before the much less used Wrap feature. In the mean time, just work around it. In this case, A cut extrude was obviously doable, so use that instead. Either that, or find another way to create the pattern besides Var Pattern. Sometimes you have to work with the tools that your given.
Submit an enhancement request. I've run into at least one other major shortcoming of Variable Patterns - lack of support for Hole Wizard features. I'm guessing they'll fix that before the much less used Wrap feature. In the mean time, just work around it. In this case, A cut extrude was obviously doable, so use that instead. Either that, or find another way to create the pattern besides Var Pattern. Sometimes you have to work with the tools that your given.