I call bullshit. Or rather, I found that part of the Fate universe general bullshit in general.
*snip*
Fully agree, and this was my main concern with Fate/Stay Night 2006. It desperately tried to give its magical aspect and the concept of the Grail War a certain level of order and structure, alongside rules which were mostly used as a means to further serve the plot and only to be contradicted upon later on. Additionally one problem I have with both shows is the underlying focus on the full extent of the role the Church has alongside the three main families, since they are both simply glanced upon and not taken into consideration and exploited to its full extent.
I wouldn't go as far and call it bullsh*t personally, but it is certainly something that needs to be explained better. Not sure if you are simply referring to the F/SN adaptation, but Zero handles it fair share of conflicts better than what Fate did.
If you do want to experience the Fate route, I suggest the VN, not the anime. The anime was just horrible, butchers too many things(including Shirou) and lacks the awesome yuri scene 
Time for me to play some VN...