(there is also the issue, that the heavy ball in the games is made from black apricorns, while the pixelmon version is made from blue ones, but thats besides the point)
Id suggest, to limit the apricorns to the seven ball types, that are actually made from them. and craft the other balls from other types of resources.
the basic pokéball disc could be crafted, by using red dye on an iron or aluminum disc. adding lapis to a red pokéball disc upgrades it into a great ball disc, and maybe blazerods, netherite or something like that upgrades that further into an ultra ball.
Timer balls could incorporate actual minecraft clocks in their design. Dive balls could incorporate prismarine or other ocean based resources. gold could be used to craft luxury balls. you get the idea.
just make the good balls (ultra balls) harder to craft, and/or to give players incentive to use the other types more.
Like in the actual game/anime lore, people used to rely on hand crafted apricorn pokeballs, untill technology reached the point where entirely mechanical balls could be mass produced.