You had absolutely no idea whether it would return or not. They didn't mention it in any of the developer build release notes. Which quite frankly it should have been mentioned. They always report what is known to be non-functional in the release notes.
I personally believe this was a test to see how the market would adapt to the change and they saw the reception was poor among testers. Otherwise there would be no harm in stating. (Pencil may not work for navigation in this build of iOS.)
A developer building for iPad Pro might want to know what functionality is and is not functional to test their apps against a build. And don't even start with "they should wait till its final" because that's a total load of bs. The Dev timelines are so short if you want to stay with the market you must test on beta software. And re-test on final.
Bottom line. It is good that Apple commented on this. At least to end speculation. One way or another.