I am not sure how the Intel XDK platform works, but the only restriction for custom Cordova plugins in Telerik Platform we are aware of is the usage of hooks. At this stage this is disabled for a security reasons, but we plan to allow it in the near future. However, there are no hooks in the cordova-plugin-zip files.
The above said, I just tried the Cordova ZIP plugin in a new AppBuilder project, targeting Cordova 4.0.0 and was able to build it for iOS. I took the master branch, so could you please retry on your side? If this fails again, please share the name of your sample project and I will test it on my side.
I hope this helps.
Telerik by Progress