It's only my opinion, but I think MilGov and CivGov would both seek to use flags, markings and symbols as close to pre-war standard as possible. Both claim to be the legitimate government, therefore both would tend to use the regulation pre-war symbols and markings to enhance their legitimacy while at the same time avoid introducing new/non-standard symbols and markings for fear that something new might be viewed as illegitimate. There is power in symbols, no small part of which is derived from their history.
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 "It is better to be feared than loved" - Nicolo Machiavelli
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