OK, so fighters can't carry cargo. That scotches my original Colonizer Rider idea... but there are ways around this sort of thing...
The changes made by Ed Kollis gave me the way out. Within your own planet type you can have two levels of colonizer - the big Highliner mount you start out with, and an "auto-colony" module that can fit on a Rider (this must be researched). The "auto-colony" represents raw materials and droids that set up the equipment and structures of the colony... just no population.
That your Highliner must provide when it happens to be in the neighborhood.
SCENARIO - A highliner with lotza pop in cargo, and a bunch of Rider Auto-colonizers docked, shows up in a system. The Riders are launched and set up Auto-colonies in every compatible world-type in the system. The Highliner visits each one in turn and drops off the required Pop to get the colonies producing - then heads back to base.
If you're doing a "hostile environment" colony, however (rock to gas or ice, etc), you're stuck with massive Highliner colony components. This makes cross-planet type colonization much harder than in the basic game (as it probably should be).
So, whadyallthink?
CURRENT STATUS...
Data files - 70% completed (colony/fighter cargo mess resolved - components and facilities still in work, most other basic data files already completed or left unchanged)
AI/race files - 10% (some changes made in generic AI files, others will follow once data changes complete)
Image files - 100% (intro screens and substitute highliner/worldship pics complete)