I suspect this is obvious, but when in doubt ...

In example 1, I have a pitching coach with a pitching IQ of 89. The range of pitching coaches in the league runs from 77-97, with a median of 88. Eight teams have coaches with a better IQ, 4 have the same IQ, the rest have a worse IQ.

In example 2, I still have a pitching coach with a pitching IQ of 89. But the range is 72-92, with a median of 83. All else being equal (i.e. other ratings that might affect coaching influence), do the coaches in both examples have the same influence on a pitcher's skill and development?

It seems like an 89 rating is an 89 rating, but I know in the past, when I want to know how good my coaching staff is, I look at the coaches relative to the league. OK, that's good to know during the signing period ... relative quality drives the market ... but over the course of the season, does an 89 coach have the same usefulness, no matter what the other team's coaches are doing?

The absolute development will be the same — a 22-yo pitcher in either case would go from, say, 74 to 78. In relative terms, the coach in Example 2 is more valuable : An average 22yo pitcher in Example 1's world would also go up 4 points; an average 22yo pitcher in Example 2's world might go up 2 points. That makes the development of your pitcher more valuable in the latter world. So the coaches have the same influence on skill and development, but that influence is average in 1 and above average in 2.

What's more important is the difference between that 89 coach and whatever coach you would have if he were not on your staff.

What I've never seen discussed for any of the ratings, either for coaches or players, is how much of a difference in ratings is statistically significant.  A difference of a point or two likely isn't going to make a difference in performance, but what's the threshold where it does?  3 points?  5?

I don't think we know much with coaches but you can find out the difference with players(if you're willing to put in the work).   It's not hard to find a player with 88/85/88/88 fielding ratings and one with 83/85/87/89 ratings.   You can compare their results(and league results for "average") and figure out what those points meant.