The <!-- is the comment indicator, this mean that everything between it and --> are not even processed by the xml engine.
*SNIP*
However this would be a mod, and i assume you want it back officially.
Yes, I'm aware of the "<!--" bit, but thanks for clarifying.
And, yes, I'm mostly wondering if it is coming back officially. If not, at the very least, Motivation V's description should be changed.
Also, there was supposed to be a negative modifier on Culling. It gives you a boost to production (which is now folded into the base trait), BUT if you used the planetary production, it was supposed to slow your growth rate whilst giving you Malevolent points in return. I can't recall if that ever worked properly or not.
Scanning the XMLs, it looks like the drawbacks for the Benevolent and Pragmatic projects were income and influence respectively.
What I am also wondering is if the reason they were disabled is because they weren't working properly. That is giving a variable amount of ideology, depending on the production on hand. I suppose I could test it myself, but I have other things on the docket I want to play with first. 
But if they did come back officially, they might make for nice Late Game sources of ideology, once planets are maxed out on population. Especially on small maps where it gets real hard, real quick to get ideological points.