https://bugzilla.xamarin.com/show_bug.cgi?id=39282#c5 reported some inconsistencies related to duplicate entries.
Following from researching that issue, I checked MSDN docs related to CreateEntry and it seems duplicate entries with the same name should be supported.
There is no restriction on the string you provide. However, if it is not formatted as a relative path, the entry is created, but you may get an exception when you extract the contents of the zip archive. If an entry with the specified path and name already exists in the archive, a second entry is created with the same path and name.
We currently do not support this feature.