The PEQ DB is run by me, and up to recently was still using the old loot system for the most part (mindrop=0 droplimit=1.) Of course, as you've come to realize this produces loot with incorrect odds since once an item is picked, the rest aren't even rolled and yes even with a randomizied list the items with higher percentages will be naturally favored. These problems existed in the old system, and that's why it needed to be re-written (there was NO way to get true odds in the old system at all.) At least now, with probability set to 100% and droplimit and mindrop both set to 0, the odds will be as true as we can get them.
The DB end is a work in progress. I recently merged Magelo's data in, and over time you'll notice our data will begin to slowly take advantage of the new loot system with accurate odds. But, we have to make sure for example NPCs don't drop too few or too many items at a time. Sadly, Magelo doesn't provide average item drop count information so we have to figure that out on our own. By decreasing and increasing the number of items per table, strategically grouping items, and by carefully using mindrop and droplimit we can begin to see drop rates that match Magelo while also keeping count in a "normal" range. But, since every NPC drops a different number of items all with difference chances it isn't going to be an overnight process.
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