No, the Modus themes are not color schemes.
A color scheme is a collection of colors. A good color scheme is a combination of colors with an inner logic or abstract structure.
A theme is a set of patterns that are applied across different contexts. A good theme is one that does so with consistency, though not uniformity.
In practical terms, a color scheme is what one uses when, for example, they edit the first sixteen escape sequences of a terminal emulator to the hues of their preference. The terminal offers the option to choose, say, the exact value of what counts as “red”, but does not provide the means to control where that is mapped to and whether it should also have other qualities such as a bold weight for the underlying text or an added background color. In contradistinction, Emacs uses constructs known as “faces” which allow the user/developer to specify where a given color will be used and whether it should be accompanied by other typographic or stylistic attributes.
By configuring the multitude of faces on offer we thus control both which colors are applied and how they appear in their context. When a package wants to render each instance of “foo” with the “bar” face, it is not requesting a specific color, which makes things considerably more flexible as we can treat “bar” in its own right without necessarily having to use some color value that we hardcoded somewhere.
Which brings us to the distinction between consistency and uniformity where our goal is always the former: we want things to look similar across all interfaces, but we must never force a visual identity where that runs contrary to the functionality of the given interface. For instance, all links are underlined by default yet there are cases such as when viewing listings of emails in Gnus (and Mu4e, Notmuch) where (i) it is already understood that one must follow the indicator or headline to view its contents and (ii) underlining everything would make the interface virtually unusable.
Again, one must exercise judgment in order to avoid discrimination, where “discrimination” refers to:
(To treat similar things differently; to treat dissimilar things alike.)
If, in other words, one was to enforce uniformity without accounting for the particular requirements of each case—the contextual demands for usability beyond matters of color—they would be making a not-so-obvious error of treating different cases as if they were the same.
The Modus themes prioritize “thematic consistency” over abstract harmony or regularity among their applicable colors. In concrete terms, we do not claim that, say, our yellows are the best complements for our blues because we generally avoid using complementary colors side-by-side, so it is wrong to optimize for a decontextualised blue+yellow combination. Not to imply that our colors do not work well together because they do, just to clarify that consistency of context is what themes must strive for, and that requires widening the scope of the design beyond the particularities of a color scheme.
Long story short: color schemes and themes have different requirements. Please do not conflate the two.