When you first 'Generate Custom Item' the option to add an ability is not there.
If you subsequently 'Generate Custom Item' on that previously generated item the add an ability option is there.
While I work to fix this issue, the workaround is this:
Don't use it on read-only items.
Make a copy of the item in the campaign so that it's editable.
When you first 'Generate Custom Item' the option to add an ability is not there. If you subsequently 'Generate Custom Item' on that previously generated item the add an ability option is there.