I wouldn't say you're overcomplicating it, per se, but you might be overcomplicating it in the wrong direction. You are correct in that there are 7 circle symbols that show up in total and that each of those stands for a numeral. Keep in mind that one of those should stand for zero, so what you have is 0 - 6 as opposed to 1 - 7. Notice that no other numerals ever show up. Nothing above 6 is possible to enter into the puzzle. It is thought that our numerical system is base ten because the average person has ten fingers. 391 in base ten is just that, 391. You're right that the grid of symbols next to it is also 391. There is no equation there. It's exactly the same number, but represented differently.
Again, hope that helps! I'll have to get back to you in a bit about the other question, cause I might need to look it up myself. I released this game in January and, as you know, we've all lived ten lifetimes since then, so my memory is a bit fuzzy.