It’s hard to interpret this new behaviour as a bug when the interactivity hasn’t changed at all by beta 3 of Apple’s next major OS release and release notes do not acknowledge the errant behaviour as a known bug. Sadly, I think this is intentional.
It’s annoying on two levels. First, the Pencil worked pretty well as a stylus input for the iPad Pro universally. Although the feature was clearly not meant to enable a new primary input device, the Pencil was good enough at it that my human nature (laziness) meant I would use the Pencil to tap on things and scroll around instinctively, rather than readjust my grip and use traditional touch input.
Secondly, even if Apple does want to limit the Pencil going forward as a drawing-only utility the current iOS betas don’t reflect that. You can still use the Pencil for some things outside of sketching or painting — you still can tap on some things and press UI buttons. You just can’t scroll or pan. If it is intentional, it shouldn’t work at all outside of a drawing app.
It’s either desired behaviour, buggy or really buggy. I’m hoping it is the latter but with just weeks until iOS 9.3’s public release and otherwise observed stability in the seeds, I am not optimistic.