It doesn't matter. Both have the same functionalities of a server. The first one (minetest) is a binary that also contains a client and with it, a graphical user interface. Minetestserver is a binary that was only compiled to have the server features, this means it can only be used over command line instructions. To not load unnecessary libraries, you should prefer minetestserver over the other, as it could use some megabytes less RAM. But performance-wise there's no known difference.
Stix wrote:where does this "minetest --server" code go?
It's a terminal command. Aka a cli command.
For those that don't know: before we had GUIs we used terminals to run and use programs. You can still use terminals for extra control, and also if the computer doesn't have a monitor such as servers.