Usually the SACD stereo tracks are entered before multichannel tracks.
However, I would ask you to reconsider adding them at all. I started like this myself, meticulously adding all available tracks into two mediums. This would of course be correct, but has disadvantages when tagging one’s one digital copies.
The layout of the release in question now is represented via a CD layer (stereo) and a SACD layer (multichannel), titled “Hybrid SACD (CD layer)” and ."Hybrid SACD (SACD layer). This allows us to use matching discsubtitles, like “Stereo mix” and “Multichannel mix” or “CD/SACD stereo” and “5.1 mix”, for example. Stereo tracks usually have the same titles and lenghts on both layers, exepcions are very rare. When tagging files this may lead to SACD stereo tracks (in .dsf format,for example) to be summed up incorrectly under "Hybrid SACD (CD layer) but for me personally this is a small inconvenience compared to be able to use discsubtitles. Those are a great help in separating tracks in software like KODI.
If you add stereo tracks to the SACD medium, discsubtitles will not be applicable since the media already have correct titles and writing “CD” and “SACD” would just be repeating them.
Also, I think the style guide says something to the effect “when track names are repeated, new media may be omitted” (can’t get the wording 100% right).
All that said, I feel that your proposed edit is not strictly necessary and your precious time might be better spent elsewhere. I would probably also vote against such an edit as the current layout for me represents the best of both worlds and to feel the pulse of my fellow multichannel editors in this matter since there are not strict guidelines yet.