There is currently no way to change the icon of the Windows export binaries, because pe_bliss (a library we used between 1.1 and 2.0) was removed because of other technical issues it caused (dependency on the libstdc++/vcredist, sometimes breaks with UPX compression).
There is also no way to set metadata on the executables either (pe_bliss could do that).
I’ll also add some info:
It is no use even if we try to use some icon editor on the exe(like reshacker, greenfish icon editor pro), after you swap the icon, the game doesn’t work anymore, guess it has something to do with how the runtime is stored under the exe as the exe goes from 12MB to a little less than 7MB
But (!) the new Icon must have the exact format and size of the original icon.
The best tool to achieve this is simply by using gimp.
Export the godot (group) icon using Resource Hacker. Then edit that file with Gimp and replace all resolutions in that icon (they’re in separate layers) by your own icon (resized).
When you export the new icon as ICO in Gimp you should be displayed an export dialogue (when saving) where you can define the exact format of every icon in that ico file. Choose the exact format like in the original godot file (here it was: 32-Bit, 8-Bit Alpha, no compression for every icon).
The new exported icon should now have the original filesize as the godot icon. Now use Resource Hacker to replace the icon.
Resource Hacker allows to uses scripts. So you can automate this process a bit from command line.