Now here's how I got this finally resolved:
- I didn't find the icons in the .app bundle, I added the icons manually there. To see the contents of the .app bundle, from the Organizer, control-click the archive, select "Show in Finder". Then, control-click the .archive file (package) and select "Show Package Contents". Under the Products/Applications directory you should find your app. Control-click your app and select "Show Package Contents". Your icon files should be present.
- I created a new archive. Product->Archive to create a new archive, then selected the new archive in the Organizer before trying to validate
Those two solutions worked together, adding the icons in the .app bundle and creating a new archive all together has validated the app and I can see the icons now good. Finally worked!