If you're tempted to do this, one thing to consider is whether this is even feasible to do with the way you intend to publish your text (cost of colour print, style requirements of a periodic, and so on). This won't be an issue if you're self-publishing on your own website, but most other ways, it's likely it will - and even on your own website, if there's anyone who'd like to print your work out, then you're setting them up for running into an issue.
Thus, colour-coding is quite an impractical method at least, and may turn out straightout impossible.
I'm afraid I don't recall any instance of colour-coding text in non-fiction. In fiction, the one I know of is the Neverending Story, where it isn't meaning of the words but whole storylines that is colour-coded. Consequently, the manufacturing cost of the book is fairly high, and so is its price in the bookshop.
Programming editors often colour-code parts of the code for viewer's convenience, but the colour isn't part of the actual code, it's automatically added according to what each part of the code does, and bears no additional information at all.
For other formatting options, bold and italics are used in sciences to denote physical quantities, sets, vectors and so on, both in equations and when the symbols are used in a sentence - where it quite helps to tell the difference between, say, "a" (indefinite article) and "a" (acceleration).
I don't recall any usage for altering the meaning of terms. Admittedly, there would probably be more of a demand for such a thing in humanities (such as your example), which I'm simply not familiar with.
What actually comes to mind as most similar to what you're trying to do is (fiction, again) the distinction between animals and Animals in the Chronicles of Narnia, where lowercase ("a horse") denotes ordinary animals we know, and capitalised ("a Horse") denotes sentient beings populating the fantasy country. It took me three books to even notice there was a difference other than context.
And yet another option I've seen is a different font type, such as Terry Pratchett used in his Discwold books to denote that a character was speaking a different language (curly font for Klatchian). He was reportedly hated by printers for it. And in translation into my language, the Klatchian lines in the curly font substituted all letters with diacritics (about a third of all letters) with non-letter characters.
One thing you may notice about the examples I've listed is that formatting helps the reader's orientation, but it usually isn't the only way to distinguish between two different things - the reader would already have enough information to figure the distinction out without any difference in formatting. And I think there's a good reason.
Whichever formatting method you might choose to distinguish between two terms where the words are identical and the terms only differ by formatting, this will make it possible to make a distinction in written text, but not in speech. What you write will be impossible to discuss in a spoken conversation. That seems like a huge setback, so I'd strongly suggest not using formatting on its own for distinction at all, but defining differing terms in words instead, such as, I don't know, "common sense thinking" versus "self-reflective thinking".