We're addressing the complaints being made about the continuity of the setting's lore.
When you decide "we're discussing what could/should/would be, not necessarily what is ," you're moving the goal posts.
One claim is that there are more combat spells than there should be. Are there more combat-ready spells than would make sense for a "profession" (for lack of a better term) that tends to avoid violence? The popular answer is, "Yes." (I disagree, but don't really care to repeat previous arguments). So, for the sake of the topic, here is a genuine continuity issue.
Why does this continuity issue exist? Probably because "flashy" tends to be more popular in a gaming context (but that's admittedly just my conjecture).
Another claim is that Shugenja are contradictory on matters religious, ceremonial, and cultural. I fail to see any examples of this having been presented from source material. When you redefine what it means to be a Priest in Rokugan, however, sure, contradictions will occur. But again, you've moved the goalposts when you do this. The setting, when taken by itself, does just fine portraying shugenja in a religious, ceremonial, and/or cultural way. When you start to compare them to real-world theology is where problems arise.