Yep, I am not exactly happy over this, Firaxis should fix that stuff so all definitions can be modular, not just a select few (ok, the majority, to be fair).
The mod size does not seem to affect this (i.e. number of changed / added xml definitions for units, civilizations etc.). Some simply do never work modular, you cannot add a single tech in a modular way, you can add 50 civs in a modular way however.
imo the most trouble for bigger mods originates from the custom dll, which isn't something I would blame on Firaxis. Your (avain) experiments with DCM come to mind here, I decided to never try to integrate DCM anywhere when I looked at the sources
Most of the changes Wolfshanze did should work ok in a modular fashion too, he just didn't go that route. I prefer to keep things modular where possible and redo them non-modular when I stumble across problems.
Oh well, here's to hoping WoC will solve that issue once and for all, but progress sure is slower than originally anticipated by the creators (isn't it always ?). I will start pushing its boundaries once things stabilize some more there.