That’s an interesting case, reminds me on this talking: https://community.metabrainz.org/t/dealing-with-physical-releases-containing-dl-codes-for-bonus-tracks/ which remains unsolved. Edits being made differently depending on artist instant and content.
As the discs were not physically linked together we could imagine splitting them (except the cases mentioned by @arifer ) but then (as spotted by @UltimateRiff) those extra discs may have to end up in a separate release group(s) depending of their content.
What is exactly on those bonus CDs? (from my searches seems older songs from Eve) If so, yes they will belong to different RGs then it may be clearer to display them as 2 CDs releases along the other ones.
PS: Then for the 2 other releases that offer only goodies (Amazon.jp version and 応援店) it could be mentioned in annotation of main release