Emoji packs often take artistic license with the ideas they are trying to represent, including flags. It is fairly rare for flag emojis to be vexillologicaly accurate. For example, the Twitter emoji for the US flag is missing 32 stars, and the corners should not be rounded. I doubt ProtonMail made their own emoji pack anyway.
Corporations have been known to hire out for content, from time to time, when communicating via emoji limits their range of expression.
As a Swiss, I never got the insistence on the square thingie... A lot of Swiss flags that people fly on their poles aren't a square either, and nobody cares. Actually, I'd prefer it if it weren't square, it always gives me this odd-one-out impression in lists of flags
Next time you feel that way just look at Nepal. By far the most unique country flag.