Gold and Jade Ore are not used for crafting but can be sold at the different Merchants for money, which in turn can be used to buy other resources, Weapons, Ammo, other [[Gear}} items, and Outfits. All of them can be found in Paititi or around the Peruvian Jungle.
That respawning gold is just similar to other respawning gold locations scattered around the city. This makes it impossible to collect right now. The icon gold does not spawn in the little alcove that it is suppose to. There are 21 different Resources - five of them rare - in Shadow of the Tomb Raider. The gold that respawns is seperate from the icon gold. Also note that the amount of resources Lara could carry was significantly higher than it is now, even with fully upgraded Pouches.
In the earlier demo versions of the game the Magnesite and Chromite Ore had different icons.