When the game reaches a place where encounters are being tuned to players with the mods they are using in mind, its time to admit mods have gone too far.
How is it "going too far" when proliferation of 3rd party mods was exactly the design goal? The WoW API was exposed specifically to foster the kind of customization we see. It's all part of the plan.
Frankly, I much prefer that model than locked-down or rigid systems that some other MMOs have, where you're very constrained in terms of what you can move, resize, hide etc. It's just different philosophies; sometimes they even overlap - in FFXIV, there are clearly delineated lines overlayed on the ground where "fire" is about to drop. The closest WoW ever got to that was AVR, back in the day, and the data that facilitated that kind of visualization was eventually hidden. Does that kind of graphic go too far? In one game it does, in the other it doesn't (and is native to the game!), but you can't judge each in isolation based on that fact alone.
To rephrase what I said earlier, it's the overall sophistication of the raid scene (including tools) that pushes encounters to higher difficulty with additional stressors - stuff like Warcraft Logs Combat Replay or Problems Pane features didn't exist a couple of years ago, but now that they do, bosses aren't falling over any faster. As shitty as the vast majority of WoD was, the actual raid bosses were strong as ever.
Also - people really underestimate the visual and room cues available to the raid. We have some dudes who raid with very minimalist setups and one guy who used no add-ons whatsoever. Granted, he was insanely good, but the point is, it's up to you to consume whatever amount of 3rd party shit you want.
Semi-related - here's a video of the no-mod guy doing one of our Heroic Garrosh re-kills in 1st person mode:
First Person WoW - Garrosh 25 Heroic - YouTube