NotJustHumanI've been searching the shops of pixelmon servers and some has shiny conversions, size and nature changes.

My question is how to people do these things? there aren't in-game commands that can do that. So do server owners change something in the server player files or something?

Its a side-mod that basically allows users to change table values and properties directly through in game commands, therefore you can use your shop auto-commands to give it to players as they donate. Unlike Ev's and Iv's side-mod i don't think this one is public, you have to develop a system of your own to do it.

Servers function on permissions, if you donate you can receive a certain feature, or
permission in this case.

Basically there are hundreds of functions in-game of Minecraft, each of these posess a permission node, if the buycraft is made correctly it'll add the permission node to your username automatically.