Media Encoder popping / crackling noises in Audio when exporting H.264 on MacBook M1 Monterey

I have dealt with a very frustrating error for the past three days. I am trying to export a 50 minute video in H.264 4k from a Mac Book Pro M1.

After the export, there is very audible popping noises starting in the video at around the 35 minute mark. These popping noises are not clipping and seem to happen randomly and they are in stereo (separately popping noises are randomly happening on the L/R channels). They are definitely not happening in the Audio file (I checked, recoded and even remixed the file numerous times).

The popping noises even happen when I am only exporting the specific sections of the timeline (but are only Audible after the exporting to H.264 or MPEG 2). Exporting these sections as ProRes seems to "work". I need a H.264 4k and ProRes is not an option.

System:
MacBook Pro (M1, 2020) / MacOS Monterey 12.6 (21G115) - Error also showed in 12.5
After Effects 22.6 + the recent Beta
Media Encoder 22.6.1 + 15.4.5 + the recent Beta

After all troubleshooting the file is now as simple as can be. It's just 2 layers:
Video: A single ProRes .mxf Video File (but I also tried it with a 4k H.264 without difference)
Audio: A single 50 minute long WAV file (but I also tried different versions like smaller MP3s etc, see below)

What I have tried so far:
- Splitting the Audiofile into multiple smaller files
- Splitting the whole Video into smaller files
- Clearing the Media Cache of ME + Clearing the AE Disk Cache and Files
- Updating ME and AE to the Beta,
- Downgrading ME
- Only rendering certain parts
- Using MP3 with various bitrates instead of WAV
- Different encodings ot the WAV/MP3
- Lowering the dB of the Audio in AE
- Exporting as MPEG-2 Video
- Changing from AAC to MPEG-1 and MPEG-2 in the Export settings
- Exporting as 1080p
- At least a few more things I just forgot

Additional Information of the Audio that maybe could influence the encoding in some way (?):
The Audio is somewhat unusual since it's a it's a very monotone soundscape with continuous bassy notes. There are also occasional "clicky" ambient sounds (like rain) as well as occasionally high pitched white noise.

To recreate the Bug:
Use a MacBook Pro M1 on Monterey 12.6 and try to export a 50 minute 4k Video in H.264 from After Effects with one continuous Audio (without pauses). After the export, you should hear popping noises starting at minute 35 in the exportet Video.

UPDATE:
I was able to "fix" the issue by NOT using Media Encoder! I just read that the recent After Effects Beta can now render H.264. I rendered H.264 directly from AE skipping the Media Encoder and it just works! So the problem is very very likely Media Encoder not working correctly on MacBooks M1...