scale_upem scaled topDict.FontMatrix in place. For a Top DICT with no
explicit FontMatrix, that attribute is the class-level default list in
TopDict.defaults, so scaling one font changed the default for every CFF
font in the process. The font's matrix then equalled the (changed)
default and was omitted when saving, so it read back as 1/1000 with the
new unitsPerEm.
Assign a new list instead, and add a regression test.