I transited with PR intl-intl at MNL T2 twice in a weekend a couple of weeks ago. Both times I had boarding passes on my phone AND physical ones, yet was directed to the desk by ground staff anyway. I went, both times they took my BP and passport and checked .. something ..?, told me where the lounge was and pointed me to security. It's not obvious to me that this step was required at all, but OTOH it only took 30 seconds or so. The desk can't be any more than 10 metres from transfer security, with a handful of arrivals immigration kiosks separating them.
This is exactly what happens. I've tried to by-pass this stupid step before with no success. It's fine if you are in Business. If you are in Economy the queue can get quite long. Particularly for the (single!) security check afterwards!