You're right that native speakers sometimes (often) don't "respect the rules" of English. In fact, we don't think about them at all. However, in the context you gave, I would consider "I told John that I had seen Jerry on Monday" would mean "I told John something. I told him that, on Monday, I had seen Jerry". It's possible that someone else could misconstrue the sentence but I cannot imagine a circumstance in which I would find it ambiguous (unless it was said to me by a non-native speaker).
For your third interpretation, I would use and expect only "On Monday, I told John I'd seen Jerry" or "I told John on Monday that I'd seen Jerry". Those statements only give the day on which the telling happened, not the day on which I saw Jerry.