It started around the time that iTunes/Safari/etc moved into their modern icon designs. It's "easier" to design for as you can get by with a generic glyph and no character.
It's worth noting that Microsoft has Mac products that actually have genuinely nice icons, though - Remote Desktop is probably just... odd.
I personally hate it as well - to the point where when I wrote a web wrapper for an email service, I went out of my way to make the icon feel more at home on a Mac. Granted, it's a shameless ripoff of the stock Mail.app icon, but I don't care.
https://dribbble.com/shots/9977474-Protonmail-MacOS-Desktop-...
Edit: a word.