I work with iPhone footage a lot. My workflow in the past has been converting the variable frame rate footage to a constant frame rate H.264 footage using Handbrake. Then I would edit that H.264 footage in Premiere CC 2018, export it as a H.264 mp4 file,and everything was fine.
This month I upgraded from a 2014 MBP (16GB, OS Mojave) to a 2018 MBP (32 GB, OS Catalina) and from CC 2018 to CC 2020. Even though I had upgraded to a faster processor with twice the RAM, I quickly discovered that my new system could not deal as well with the H.264 footage as my old system could. I've still not figured out why that is that case.
Since I can no longer work with H.264 footage, I switched from Handbrake to Shutter Encoder to convert my VFR footage to CFR. While Handbrake forced me to convert to H.264, Shutter Encoder allows me to convert to ProRes 422 LT (as well as tons of other codecs). So I imported my CFR footage in ProRes, and everything cut together fine.
But then when I went to output the finished product in H.264 (for viewing over YouTube, Insta, etc), I saw in both the Premiere export window and Media Encoder that the footage was WAY overexposed (pic atached). However, if I clicked the "Match Sequence Settings" box at the top under Export Settings, it would output correctly.
I cannot understand what is going on. My workaround for now is to export as a Prores Quicktime, and then convert the QT file to H.64 MP4 so the file size is more manageable for internet disribution. But I cannot understand why this is happening, and it's a pain to have to go throug that extra conversion process. Anyone have any ideas? Screenshots attached.