And so here again: It has nothing to do with sector alignment for CDs.
The JUNK chunk is there to reserve additional space after the 32-bit RIFF header, so that the 32-bit RIFF header can be overwritten with a header of a 64-bit file format, like RF64 (RIFF, 64-bit - as specified in “EBU-Tech 3006-2007”) or BW64 (Broadcasting WAVE, 64-bit - as specified in “ITU-R Recommendation BS.2088-1”), in case the file gets larger than ~4 GiB during recording.
Obviously, the 64-bit file formats have larger headers, because they have to accomodate for larger length fields. Therefore, when starting out with a 32-bit RIFF WAVE file, it is often wise to reserve some additional space in case you need to grow the headers afterwards, when the file gets larger. The JUNK chunk marks that space as reserved (and to be skipped by utilities reading the file) until it’s needed.
The specifications above explicitely mention reserving space after the 32-bit RIFF header for the 64-bit extensions using a JUNK chunk and, as the file gets larger than ~4 GiB, overwriting both the 32-bit RIFF header and the following JUNK chunk with the header of a 64-bit RIFF extension.
I agree with you that it should be possible to turn this off though, since, as you mentioned, especially hardware units often won’t implement the full RIFF specification, but instead expect some sort of minimal or “canonical” format where certain information is stored at some very specific offsets - even though the “full” RIFF format itself is actually very flexible and “dynamic”, and allows almost everything to be “relocated” inside the file.