Good news.
Our app is now available on the Mac Store and Apple finally approved the MacOS app.
Long story short, for whomever runs into the same issue and has the same question... Just continue while not seeing an icon and submit the app.
Tell to have Apple review the app and after that process the icon magically appears from then on, also inside Application Loader.
Thus, the icns file was perfectly fine. Somehow this is/was at Apple's end, and in the end, nothing to worry about.
Hope this helps!