Well, having a unwinnable fight against a end/late game boss early on is a classic RPG trope. Helps showing character growth and helps preventing excessive power creep.
Only real problem I have with both this and the 2 Zenos fights is that they lack any actual sense of "oh crap, he's too strong" danger. You just have to hack away at an inflated health pool until they get bored and one-shot you with an attack you easily tanked the first time they used it