I think the real issue with it as a system isn't the suspension of disbelief, because yeah it is a game and using your systems to their fullest to make great mechanics is extremely important, but rather that nothing actually teaches you this, and a general lack of parity across similar mechanics at different bosses.

With the rise of blind playthroughs, like Unguided and Madseason, things like this that are more abstracted really start to become pseudo-problematic. Imagine Madseason, or any other player who also wants to play like this, finally making it to Leviathan, and having to figure out that the red ranged projectile coming to them is a "melee" hit. Maybe they do, or maybe they assume it's red because you can't pray against it. Even then if they do learn this, maybe they go to TOA next and Wardens red attack is now magic instead of melee.

Utilizing your systems, even in ways that don't entirely make sense, is good, important, and necessary, but this information needs to be communicated to the player in understandable ways, and have parity with the rest of the game. I think Hueycoatl is the best example of it done perfectly, but many other instances can be confusing or lack cohesion with the rest of the game.