I did have to show the PeduliLindungi app to United when leaving the US last week (it was on the United Airlines checklist in order to get my boarding pass), but no one has required it since on way to Raja. United just made sure I had it, didn't check that it was fully working or anything.
Obviously authorities in Indonesia have looked at my vaccination card at least once, maybe twice while I have been here. I know they looked at my paper vaccination card at immigration when I arrived in Jakarta, Batik Airlines probably also looked at it in order to check in for flight to Sorong but I don't recall specifically. No one required anything for ferry from Sorong to Waisai, but boarding there was so haphazard someone else might experience something different (though I doubt it)