1. No transpose -> Yes
What? Yes No? Right. If you are used to Windows you find this just as logical as "Do you want not to delete this document -> Yes/No?" If you only use Macs you can run into a brain-problem. To avoid this, activate the little box on every instrument track (preferably in the template) if you want to keep your own notes in your own music.
Mhm, why not "Transpose Yes/No?" Too simple!
2. Global Chord Track -> Display only
This is partially related to the pet above. If you don't have this checkbox activated, make sure that there are no heavy objects or weapons within your reach: Your notes may follow the chords in the global track. And they will not return to their original positions when you turn this option on after your notes have been moved. Again, best is to set this in your templates.
I do not know why Logic sets both options to change our notes by default. I believe it wants to make its own music and sees us just as disturbing elements.