In the context of the Small Craft feature?
In that case the "excess space" is what is left over after the rest of the design requirements have been met (drives, fuel, helm). So it is part of the stated tonnage.
For example the 20ton launch has 13tons of excess space. I break it down as:
4tons helm
1ton maneuver
1ton powerplant
1ton fuel
13tons excess space
20tons total
Excess space is what is left for the end user's purposes. Cargo, passenger seats, staterooms, vehicles, turret, computer or whatever will fit.