Now it is not possible. The icon is extracted from the link or from the exe file. Maybe in one of the next versions we will make application icons configurable.

I see one way, but it will not be working for every application:

Try to create desktop shortcut for the application on server's desktop, then change the icon in the shortcut. Now run Winflector preferences/Applications and publish application using created shortcut by clicking [...] button.

Mirek