As we all know, mobile factories such as carriers, czar's and fatboys cannot combine building with moving or attacking (or more specifically: selecting a new target). I understand it's an engine limitation.
However, would the following be a good/feasible work-around? :
When selecting a unit to be built, it is built instantly (this could be implemented simply by giving the mobile factories very high build power). After this there is a 'cooldown' during which no units can be built. The cooldown period is equal to the buildtime of the unit previously built, or if the latter is not possible, a constant cooldown can be used.
While not the ideal solution, the mobile factory unit is now only interrupted for a split second when popping out a unit.
It might be hard to combine this with build queues, but I for one could live without them on mobile factories.
Note also that the insta-build means a sharp sudden hit on your mass and energy storage, but I don't see this as such a problem. In fact, it fits quite nicely with them being 'experimental' factories, and would put greater focus on building storage.