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Well here's what it says on Bulbapedia in regards to obtaining the blocks: After the player has both received the National PokéDex from Professor Oak, and 3 hours of gameplay have passed after completion of Baoba's second challenge, Baoba will call the player to tell them that he has come up with a new idea for the Safari Zone. After receiving this call, the player will be able to place blocks in each active area of the Safari Zone. Each active area can contain up to 30 blocks at one time. Initially, the player will have access to only 6 block items. After another 3 hours of gameplay, Baoba will call the player again and add 6 new blocks. This cycle will repeat 2 more times until the player has been granted access to all 24 different block items. So it's time-based going by actual game time, not the clock. That being said, as far as I'm aware, there is no way to edit the Johto Safari Zone currently in PKHeX, though it would certainly be a very useful feature to have in the future (particularly as a shortcut to the crazy long time it takes to level up the Safari Zone blocks needed for certain Pokémon).

I'll be doing that later on, not to worry. edit: