As an example, let's take the plugins for the Rust game: in it, the plugins for teleporting home and teleporting to a saved point use different commands without a prefix. And the data about the author of the plugin is registered inside the plugin. Extra prefixes deprive of convenience when using the plugin.
I do not think that the /sethome and /home commands will be used by other plugins that do not relate to teleport.
using a prefix is the way to go. when a /command is used it triggers an onplayercommand method for all plugins. i ran into an issue where it was reading from the database from 2 of my plugins for every command entered. a simple fix was to add a prefix. so something like this:
in my case it was just getting a database connection for both plugins. but if your doing something more complex you can cause errors in other plugins.
with the above code it prevents any errors that may happening.
also with the api being new there is alot of development going on, the odds of having multiple plugins using similar commands is quit high. in my case there will be a /sethome player position, /sethome area, and /sethome area npc so my prefix's will be /npc, /player, /Area fallowed by the sethome.