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Imo it should just be a range of drop chances, that come to a balance for their lvl across the dungeon.
If there's 10 rooms with lvl40 mobs - 6 of those rooms can have different types of mobs with, say, 0.1% chance to drop a crafting material for one of 3 pieces (or sets) of gear.
Then 3 rooms would have 24+-3h respawn bosses, each having a 50% chance to drop full mats for a single craft of a single piece of gear or several mats for different pieces within the set that relates to it. And maybe 1-3% chance to drop a full piece of gear.
And one room would have a 2d+-5h respawn boss that drops mats for all 3 sets and has a higher chance of dropping full pieces.
When the boss rooms don't have bosses in them, they're populated with mobs that have the same loot tables as the bosses, but the chances for that loot are lower than the ones in the "normal" rooms, so the overall daily chance is the same, but the ones farming the boss room would also be the first ones to see the boss respawn and would have the first dibs on it.
At the end of the dungeon there'd be a super cool and hardcore raid boss with a several-day respawn timer, great chances to drop mats and full gear, and some sort of unique piece of loot.
In other words, every room would be pretty much equal in its worth on the grand scale, but boss rooms would give you an edge over the others, so for several hours every day there'd be a higher concentration of players in those rooms fighting for the chance to be the first ones to kill the boss.
Chances would obviously have to be properly calculated and balanced and all that.
just wasn't really a thing in my neck of the internet woods.
L2's pve was definitely reaaaal limited before the later updates where they started imitating WoW.