despite the fact that the human eye doesn't see it as particularly distinct from its neighbors
Color is culturally based. It's not so much that the human eye doesn't distinguish the color, but that our culture doesn't treat it as a distinct color. For example, Russians have distinct words for light blue and dark blue, segregating them into distinct colors where English speakers tend to just see 'blue' and not distinguish as much on hue.
There have been several studies about how perception is influenced by language. It's not that the eyeball works differently in different cultures, rather that the arbitrary lines our different cultures have between regions of color space determine how we define various colors.
In Newton's case, it's possible that Indigo was a separate, well-defined color region that we've since lost in common usage. The color still exists, we can still distinguish it as unique when placed between it's neighbors, but on it's own we'd probably just call it either blue or purple. I'm not suggesting that Wikipedia is wrong about the history of ROY G BIV and Newton's fondness of the number seven, just that language defines our perception of color simply because in English, we have common words for those colors. Seven is pretty arbitrary, but so is three (RGB), four (CMYK), or five (Hexachrome). It all depends on why you're categorizing colors. This isn't even getting into gamuts or color theory. The human eye is based on red, green, and blue receptors, but that's just a physical adaptation to allow us to see all colors in our visible spectrum. We're more sensitive to some colors over others, but there's no reason we couldn't see indigo as a distinct color other than that in our culture it's not all that common to distinguish it as separate. There's no reason there should be six arbitrary colors in the rainbow rather than seven, eight, ten, or twenty.
Take teal, for instance, another rarely-used color. Some people will call it blue, others green. Still others will just call it teal. Our language doesn't change the color itself, just how we categorize it.
The idea that there are only seven distinct colors (or any arbitrary number) is silly when you take language out of it and just apply numerical values to colors. What color is #fc0? Yellow? Orange? Orangish-yellow? What is the exact wavelength of 'red'? What color is at 450nm? (Hint: it's somewhere between yellow and green). The seven traditional colors of the rainbow are all about 20-40 nm apart except yellow and green, and red and orange. There really should be a color in between, and in some cultures there are.