Just for the record, the OP symptoms sound like a known issue which began on Apple Silicon around Sonoma 14.4. It reportedly did not happen on Sonoma 14.3.1.
It is not an FCP problem but an issue with ProRes 4444 encoded by older versions of the third-party FFmpeg utility. On Apple Silicon, this causes the "opaque alpha" behavior described by the OP -- on current versions of FCP, Resolve Studio and Premiere Pro. It doesn't happen on Intel.
It also causes ProRes h/w decoding errors in the MacOS system log (AppleProResHW), although no user-facing errors I've thus far seen.
These system log errors are not visible from the Console app, but only by using the terminal command "log show". That command produces verbose output so it's best to constrain it to 10 seconds or so, then filter through the output using BBEdit or another programming editor with good filtering. Example of error:
2024-05-11 09:53:39.630131-0500 0x2db Error 0x0 0 0 kernel: (AppleProResHW) ERROR: AppleProResHW (0x59cd9b0a): processDecodeFrameDone(): HW error decSatus=6 status0=0x7f043000 statusCode=63 status2=0x1
Example of "log show" syntax to view system log messages from the previous 10 seconds:
sudo log show --last 10s > ~/Documents/LogShowOutput_10s.txt
Given the original ProRes 4444 file produced by the older version of FFmpeg, it's possible to determine its origin by examining it with MediaInfo or Invisor. Under "Writing Application" it will state the Lavf library version used by FFmpeg to encode the video. Status of certain versions:
FFmpeg 7.01, Lavf61.1.100 - alpha channel OK, but causes ProRes h/w decode errors in MacOS system log
FFmpeg 7.00, Lavf61.3.103 - alpha channel OK, but causes ProRes h/w decode errors in MacOS system log
FFmpeg 6.10, Lavf60.16.100 - opaque alpha channel, also causes ProRes h/w decode errors in MacOS system log
FFmpeg 5.??, Lavf58.43.100 - opaque alpha channel, ProRes h/w decode errors in system log
However, if a ProRes 4444 file generated by the older version of FFmpeg is later transcoded by an NLE or some other utility, the opaque alpha channel will be "baked in", plus the originator of the file will be wiped out. So depending on the post-production sequence, someone might tell you the file came from Compressor, FCP, etc, but it originally came from FFmpeg, you just can't tell anymore.
This problem was reported recently by a customer using Ross Video Xpression Incoder, which internally uses FFmpeg. That software is used in the broadcast TV industry, especially for real-time graphics rendering and video processing in live broadcast environments.
Non-Apple versions of ProRes are not supported by Apple, but Ross Video is apparently a licensed ProRes application developer, at least based on Apple's support site: Apple ProRes and ProRes RAW Authorized Products - Apple Support
I've been examining this the past few days. Monday I'll contact Apple support and Ross Video to notify them.