Even though ZUN said this, it doesn't really mean it's an actual language commonly used in Gensokyo. What's used in ancient magic books and what's spoken are two entirely different things. Yes, it does make more sense that said "random scribbles" could be jindai moji. It still doesn't mean that any written scribble is going to be jindai moji. You can continue to believe that everyone knows what they're talking about at any given time and continue to research it, but I'll just sit back and not care about the whole thing :P
It is at the very least interesting that you made that correlation. If it proves to be useful then cool.