This is how I imagine Nintendo is setting up their Online Network.
You log in to an account attached to your My Nintendo that has a username and password.
Once logged in you will have access to the eShop, your friends list, chat, etc etc.
Everything will seem very unified behind Nintendo from the Users point of view.
You go into the shop, you see games listed, you can buy them, download them, play them.
You can insert a disc into the drive and choose the option to go online.
This is where the portal comes into play.
You chose to play BF3 so it routes you through Origin servers which handle all the cross talk, chat and online play.
If you chose Killer Freaks, it routes you through UbiPlay
....Valve's Black Box routes you through Steamworks
etc etc.
From the users standpoint, you won't really be able to tell the difference other than the logo that will pop up before you start playing.
You decide to download a game or some DLC
depending on who made the game, it will route you through which ever portal is hosting that particular game or DLC and you download it through there. Eitherway, you wouldn't even notice you are no longer on Nintendo's server except for a logo that would probably pop up while you are waiting for the download to start (think like a startup logo before a game).
This is why I think alot of software is gonna be running through the Steam portal (assuming it works anywhere near how I imagine) as I assume it will be multi-plat and will likely use the PC build as a port which will already be Steam enabled for the majority of games.