Hi there! Thought I'd chime in.
So with regard to .m4a files - in ffmpeg, ".m4a" triggers the "ipod" format, which changes the listed major/compatible brands of the MPEG4 file, and I believe restricts codecs to be iPod/iPad-compatbile. You should be able to create an MP4 and rename it M4A, it'll change the major and compatible brands but otherwise be a valid MP4 file.
Here's some of the output of boxdumper on an m4a. I'm just looking at the file type box, because I'm somewhere around 99% sure that's all that really changes, but I'll admit I haven't combed through every single box.
[ftyp: File Type Box]
position = 0
size = 28
major_brand = M4A : iTunes MPEG-4 audio protected or not
minor_version = 512
compatible_brands
brand[0] = M4A : iTunes MPEG-4 audio protected or not
brand[1] = isom : ISO Base Media file format version 1
brand[2] = iso2 : ISO Base Media file format version 2
Whereas here's a normal MP4:
[ftyp: File Type Box]
position = 0
size = 28
major_brand = isom : ISO Base Media file format version 1
minor_version = 512
compatible_brands
brand[0] = isom : ISO Base Media file format version 1
brand[1] = iso2 : ISO Base Media file format version 2
brand[2] = mp41 : MP4 version 1
Also, I did some testing with Safari and that FLAC-in-MP4 file. I figure what you're mostly interested in is working with HTML video + audio elements? Just clicking the link played the video + audio, but I figure that may not be quite the same as using HTML5 video + audio elements.
I made a quick webpage:
<html>
<head><title>FLAC-in-MP4</title></head>
<body>
<video controls><source src="test-FLAC-in-MP4.mp4"></video>
</body>
</html>
Served it up using good ol "python -m SimpleHTTPServer", opened the page in Safari - video played, audio played.
Then I converted it to an m4a file using ffmpeg, using "-f mp4" to override that "ipod" format:
fmpeg -i test-FLAC-in-MP4.mp4 -c:a copy -vn -strict -2 -f mp4 -movflags +faststart test-FLAC-in-MP4.m4a
(I also tried it without the "-movflags +faststart" flags to be thorough, though in most real-world scenarios you'd want to use that).
Similar concept - made a simple audio page:
<html>
<head><title>FLAC-in-M4A</title></head>
<body>
<audio controls><source src="test-FLAC-in-MP4.m4a"></video>
</body>
</html>
Served it the same way as video, and it played without issue.
I've also done some testing with using hls.js to stream FLAC in a fragmented mp4 stream. I had to modify hls.js (I have a PR open here: https://github.com/video-dev/hls.js/pull/4772) - that worked in Safari as well.
I also tested your MP4 using Quicktime Player, the default video player - FLAC audio played back fine.
All working in Version 15.5 (16613.2.7.1.9, 16613), which corresponds to macOS 11.6.6 (Big Sur) - I'm behind by a major release, still.