Master Quest - Does it reinforce the temple order?

Well, I went to the dungeon walkthroughs of zeldadungeon.net, and did some simple text searches:

• I don't see any references to the Longshot in the Fire Temple.
• I don't see any references to the Megaton Hammer in the Water Temple (or the Ice Cavern).
• I don't see any references to the Silver Gauntlets in the Shadow Temple.
• I don't see any references to the Hover Boots in the Spirit Temple.

This makes sense to me; while they can redesign puzzles, they can't/didn't change the fundamental rooms at all, so finding new places to stuff huge blocks/large gaps would be challenging. (The only possibility then would be adding hammer switches, but I'm not seeing any.)

I'll say you're pretty much good for either order.