I don't think I've ever had a perfect exploration score. I always make sure to uncover all the corners after the robot bossfight. No idea if that is even needed.
It does count toward the final score, as does searching all of level 5 even if you beat Goo and find the Rat King. If you don't search the entire level you lose points.
The wiki says that for the exploration score you only need to reveal all hidden doors, items, open all containers (except crystal chests), solve all puzzle rooms, complete sacrifice rooms, etc. You don't need to explore boss rooms fully afaik.
The key to getting max exploration score is to go Warlock (for unlimited food) and use whatever means available to collect a bunch of scrolls of foresight (ring of wealth, parchment trinket, recycle spells) as you descend the dungeon. Then after you kill Yog (but before picking up the amulet) go back through the dungeon and use your scrolls of foresight to find everything. This means exploring every secret room and solving every puzzle room (looting the treasures in gas filled rooms, sacrificing enough enemies on the altars of sacrifice to get the weapon, etc).
Leave no treasure chest unlooted, no barricade unburned, no animated statue alive, no grave undisturbed! All keys must be used up, all magical fire walls extinguished. Loot everything!
Then you can go back and grab the amulet for your usual ascension run. The reason the Warlock is so good for this is because he can feed himself just by attacking enemies. He doesnât rely on drops which are turned off for each enemy when his level gets too high above theirs. Warlock can also take the beacon from the dwarf kingâs crown upgrade and use it to teleport around faster, but thatâs not really necessary.
You can of course do this on any class if you find a ring of wealth and farm a ton of food and scrolls. Or you can try finding everything on the way down, exploring the intended way (especially with the rogue or a talisman of foresight). But this is more error-prone and especially tricky to pull off if youâre playing 6 challenges including on-diet (because you want to get a high score).
Although I stayed with the Sniper, using your suggestion, after several unsuccessful attempts, I was able to get a perfect exploration score. I didn't get the talisman, however, I was able to gather several Mind Vision potions and convert them into Magic Sight. I discovered 2 hidden rooms I had missed.
The other thing is what ProjectingSpiritBow pointed out - in my haste to stay alive on such a daunting run, I discovered, but bypassed, several alter rooms. I may be a developer but I try to avoid spoilers and so never looded at the Wiki... aside from which, it is Wiki, and anybody can put anything there (unless it supports the American Constitution and removal of domestic terrorists usurping positions of servants to [We] the People, committing sedition to undermind America, and calling these terrorists out for treason over their criminal conspiracy to deny Rights while acting under color of law). Politics aside, it seems that was the missing element. You can't just find the rooms, you must also use them to reveal the treasure.
Sadly, although I got gold scores all the way, it was still not a perfect game.
Tengu managed to get in a stike.