Beating the 2nd best usually doesn't do much, considering 2nd best is usually opinion.
For the RJJ situation, his legacy wasn't hurt much by not fighting him. He was a master at 154, unbeatable at 160 and 168 (noone head to head can be RJJ at 168 even today), at 175 he dominated (with the exception obviously), won a title at heavy, then regained the lineal title at 175. In the case of 175, it's not as if people viewed them as equals, he was just seen as the next guy who was seen as the best challenge to Jones. Noone would bet against RJJ in reality.
For the Klitschkos, it'd damage their personal image, something that means a lot to them both, especially Vitali, if they ever fought. In boxing terms, hmm I guess so. But Wlad and Vitali were never prime-for-prime. In an in-depth boxing analysis on that fight, thered always be doubts that one wasn't prime.
The Mayweather/Pacquiao fight situation is just embarrassing. Mayweather's legacy is more damaged from this, as it has been years since he has universally been ranked 1 P4P. Pacquiao will remain a star outside of boxing, a huge celebrity in the Philippines. I can't see what Mayweather will be outside of boxing.
But i'm sure it does devalue other legacys in some form or other. Its just these examples can be explained otherwise.