Thank you!

Found a global variable named "dragon returned"; put it to 0 in the two types of events (change location and script) related to dragon attacking and flying by. I just need to try the mod now. If it works...

Wait, wait! Before you upload anything (and credit me for messing up people's games). If you change that condition to 0, then dragons will
stop appearing when players proceed along the main quest line, once it gets set to 1.
I had assumed this was just something you wanted for your own playthrough. If it's something you intend to share and that global is all you needed to change to get it working, a more compatible way to accomplish this would be to leave the Story Manager stuff alone and instead just change the default value of the global from 0 to 1. That way, dragons will appear from the start and also after the Whiterun dragon; and it won't conflict with other mods that may edit the Change Location nodes in Story Manager.