Welcome to Nasomi. You'll soon find that Yughott is not the only zone that is messed up in some way(looking at you Monastic Cavern). The change probably wasn't done on purpose unless it was to fix exploits that were being used.

Remember, this is a private server and is still a work in progress, yes a lot of things are retail accurate. But there are still things such as the mining you're experiencing littered throughout. Some of those are "good" and some are "bad".

Lizard Molt is also abundantly present in Palborough Mines, I suspect it's because chocobo digging doesn't work he had to throw it in somewhere, similarily since gardening doesn't work elemental ores are in shakrami, ifrit's cauldron and havlung (possibly ahtowa too idk never looked or tried for).