You will still have the ability to automate the PJ's and Quarry's and level them up but instead of having hundreds of them placed on the map by players you will be upgrading and using the public ones on the map
I fail to see how this is going to make it harder as lets be honest the placement of the player owned Quarry's were a nightmare and trying to Automate them could be just as bad sometimes, If anything this is going to make Automating the Quarry's and PJ's a thing of ease, You will buy the Pj's and upgrade the public ones then using the Item from the black-market automate the PJ's and Quarry's from the comfort of your base.
The removal of the VIP perks from our Pure servers is not something that we wanted to do but with Pure been a community server the changes made to Facepunches TOS made it so the VIP perks had to be removed.