Can you send individual emails or PM to special members when a user is awarded? It's not a part of the default functionality but I do believe that you can add that through the Rules.
Is it possible to build 2 independent award systems inside the app? F.e. one for regular members and another one for a commercial group? If you are talking about making it to where certain things show up depending on the usergroup? That is not a feature, no. You can have awards that can only be awarded to members in specific group.
What is the initial award routine, when you first run the tool? Does it initially reward the conditions in the past? The only tool available is the one that allows you to upgrade from previous award systems (Awards by pederfi or HQ Awards). The Rules app, with correct Rules setup should be able to suffice this as well though.
Anybody has a recommendation for award image creations, f.e. png with transparent background? What is the best graphic format to look good on light and dark skins? That is personal preference. I prefer PNGs and normally designing them with a glow or border will make them stand out on either depending on if the award is light or dark.
Are you planning to do upgrades for a long time? We plan to do them for the foreseeable future that I know of.