Johannes Schindelin [off-list ref] writes:
IIUC then each conflict hunk is handled _separately_ like this: the
lexicographically smaller between the two file sections is displayed
first, regardless if a previous hunk had a different order. Not that it
matters most of the time, but isn't this dangerous?
You are probably right. Probably the right thing would be to
use the first hunk to determine the flipping order and stick to
that for the rest.
Not that I've seen problems with the current behaviour, though.