The entire experience is a whole, the stage IS part of the boss. You beating the stage and getting back to the boss is just beating phase 1 of the boss fight.
The issue is when the stage becomes trivial, is too hard, has annoying/cheap sections in it, or is too long. All of these are equivalent to the boss itself having too much HP, being too unfair, having cheap moves, ect. because again, it's hand in hand and the boss IS the stage, just another phase of it.
If the run is challenging, thought provoking, and a fair length, then I have no issue with it. A lot of the runs are just bad though and they end up being too long or too short, and it just breaks the whole idea around it.
I don't think From have perfected this formula and I do find my mind wandering on re-runs and just feeling annoyed rather than worried about getting back to the boss to not lose souls (or even just make it). I think the series could use a bit more playtesting in their final bonfire placements before the bosses. As of now, if I had a vote, I'd just vote for an instant retry of the boss with no load screens. Just reset the fight, starting positions, ect.