Technically FFmpeg doesn't even support creating .mp4 with LPCM (even though some players will play it back anyway), so I'm not sure how it came to be in the first place. Reaper used to default to .mov up until I'm not sure which version (I skipped a few versions updating to 6.68)
https://avidemux.org/smif/index.php?topic=19861.0
I did a little bit of research and found that while it used to be true that .mp4 didn't support LPCM, the spec has been revised and it does now. On the other hand, .mov has always allowed it and is widely supported.
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