Your example of "no, yeah we're all out" doesn't actually work, because the "yeah" is dangling. The "yeah, no" works (the yeah agrees with the question, we do serve Pepsi, but the no modifies it because we're all out).
and the same for the "yeah, no" in the second example - the "no" is dangling.
but yeah, it can be confusing if the tone of the original question implies a negative (like "you don't serve Pepsi here do you?").
took me ages to work out that the first value doesn't matter ;)
“Do you serve Pepsi here?”
-(no) “yeah no, we are all out”
-(no) “no, yeah we are all out”
-(yes) “no yeah, we got it”
-(yes) “yeah, no we got it”