"In comparison" is entirely relevant to Aldarc's point, which was spelled out for you in the very post you quoted. The high-end NPCs listed can't go out and solve the problems instead of the PCs: If they are even aware that there is a problem, they might be trying to hire the PCs to solve it.
Given its Eberron, they might even be working against the PCs instead.
So no: they aren't going to overshadow the PCs simply by virtue of being high-CR creatures living in the same setting. Compare, as was suggested to you, to Forgotten Realms where there are several high-CR beings known to actively solve problems by doing essentially what the PCs can do, only better.
Eberron tried a lot of new things. Assuming that PC's are special snowflakes and no one else in the world can gain class levels easily except the PC's was one of them.
And if you like that concept, great. Go play Eberron.

Or import the concept into your campaign and say that Elminster is normally a 5th level wizard, but while he's the Chosen of Mystara he's an Archmage who gives out random quests and sleeps with goddesses.
But I think faulting the Forgotten Realms for not using a a concept only a single, brand new (at the time), setting uses isn't really fair. It's not like Dragon Lance didn't have a God wandering around helping out the characters in the stories, have a PC become a God. Or Greyhawk doesn't have a dozen or sight high to epic level characters wandering around, some of whom also became Gods.
Because most settings seem to assume that everyone can gain experience and levels and PC's aren't special in that regard. PC's just do it faster than everyone else because they are being controlled by extraplanar intelligences that don't allow them to take breaks or settle down to a quiet life. Everyone else takes months or years longer, but they have a head start.
High Level NPC's are just one of those things you don't examine too closely, like the D&D fantasy economy. Gold and magic items just appear because PC's are killing stuff. High Level NPC's appear because the PC's are either ready to deal with them, or need to be reminded not to run roughshod over all the common NPC's. Some of them have backstories, some don't.
But I don't see how they would make the PC's feel less useful. We have stories about legendary athletes - does this discourage talented new athletes from trying out for the big leagues? And the PC's have a real chance of surpassing any of the legendary NPC's if the game lasts long enough. Or they may just remain as stories, and the PC's never meet them.
The problem is when the DM insists on having them show up for low level PC's. For any reason - being their special friend, putting them in their place, or even just giving them quests. It's using a sledgehammer to swat a fly. Massive overkill and causes a big mess.