I don't really see how combat balance being fragile, as he calls it, is a bad thing. It's meant to incentivize different playstyles yet let them all accomplish what they set out to do.
The example of accidentally taking down one of the bosses in seconds with the Master Sword really sticks out as a "Well, what did you expect?" moment. That's an Explorer reward. By exploring the world and finding the legendary blade, you unlocked the ability to cheese boss fights. The ability to drain all challenge from those fights are so hardcore explorers can skip their least favorite parts. Likewise, if you just want to beat the game, you can just outright rush the bosses with no Master Sword, no food, not armor and win with skill alone. Both are valid playstyles, and both beat the boss. One uses hours of preparation, the other uses reflexes and combat skill.
Essentially, the more non-combat stuff you do, the easier combat gets. By design. The more you explore, the sloppier you can fight. Up to the point where nearly any boss can be dealt with very easily. So complaining that your exploration rewards makes combat easier, when you did 30 hours of exploring and not fighting bosses.... well yeah. If you wanted to fight challenging bosses, they were right there the last 25 hours. Why didn't you?