MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
I don't have the Z-stop installed since I'm using a proximity sensor. But you are right. The option should be made available.
I'll make changes to accommodate the Z-stop later today.
In the mean time you might just want to cut some long slots to the part starting where the holes are.