So, the way it works is that the console mod handles loading all commands and their classes. The commands.csv tells the console where to look for these scripts (the
class row) and how the player uses the command (
command is what they enter to use it,
syntax and
help are shown by the "help" command, and
syntax is also shown to the player if the command returns CommandResult.BAD_SYNTAX). It doesn't know or care if these scripts are loose or in a jar as the actual class loading is done through Starsector's classloader (which supports both).
Since the console mod handles everything, the CSV won't be read and nothing will be loaded if the console isn't enabled in the launcher. Java only loads classes when they are needed, so don't worry about including commands in your mod's jar.
The sole exception to the "don't worry about creating a dependency" rule is any loose script in data/scripts, which is a magic directory whose contents are automatically compiled by Starsector when the game starts. That's why the tutorial recommends putting scripts in data/console, so you don't accidentally create a dependency on the console mod. The tutorial doesn't mention jars because it's old and was written before they became commonplace.
tl;dr: commands can be in jars, don't worry about creating a dependency, the tutorial is outdated.