I doubt Steve ever considered people building 'mini' PDCs, so since prefab PDC components have a fixed size, I assume the game's internal math combines smaller PDCs into one, larger, prefab component. And the separate code that creates PDCs out of components assumes a minimum of one component-per-PDC.
So, yeah, you've outsmarted yourself (or Aurora, or whatever) and your mini-meson bases are going to suffer significant 'construction attrition'.