So I'm not sure if anythings changed or if i flukily got the items needed before beating hoenn... but when i went to 114 to start the quest, i was able to pay the 100k straight away and the first site i went to was allowed in.... as for spawns, im getting all types. Got cubone and houndour in same site. Was getting pawniard and noibat in another. Wailmer and something else in another site. It doesnt seem like theyre time based, but more luck. I feel like its similar to headbutting tree's where time doesnt matter, its just the rarity of it appearing.
Also, its currently 2.5k to enter each site.
EDIT: Most of those poke's I mentioned did run. So I think the shiny rock is exclusive where the pokemon doesnt run since its a paid item you need to use to break that piece since a Tyrogue was running from everything i broke, then the shiny rock I was able to catch it. This was on my VERY FIRST excavation with less than 100 excavation points! I now have 230
EDIT 2: Confirmed... on my 4th excavation, nosepass was flee'ing at every rock. he appeared at the shiny one where you require the pick axe and he didnt run from that encounter.