In my mod, I use the three unused tech spaces in the list to add three new techs, each of which adds a new unit, with custom graphics, which cannot be built in the workshop and have more special abilities than player-designed units can have. So I think there is some use for using the three available tech slots to add new special units. You can also have some faction(s) start with such techs so they have a unique advantage at game start.
If scient resumes work on the unofficial patch, this capability will be greatly enhanced, as we will have a way to add new units to #units which can have any level of reactor and which can be flagged as AI-only and/or not reverse engineerable. (Currently to make a custom unit not reverse engineerable, you have to give the unit a psi attack.) So let's hope he picks it up again - it will greatly enhance modding capabilities.