Accessories are never included in MSRP - it doesn't matter whether you buy them with the vehicle or not. But lots of people do get confused about this and talk about dropping items from their order to stay under the $80k limit. It's not good for Rivian to have people confused into buying less ...
In reality, this change affects nothing. They're not charging you any more or any less for your "roof rack" (cargo crossbars), but now at least you can decide when you want them delivered and you can track the package.
Accessories are currently drop shipped separately from the vehicle, and can arrive earlier than the vehicle (chargers, mostly) or much later than the vehicle when there are supply problems (e.g. all-weather floor mats). You get no notice - I had my charger shipped after I left town for two weeks and it was delivered and left on my front porch for more than a week while I was gone. Yikes! Fortunately it was still there when I got back. If I had the ability to order the charger separately, I would not have had it shipped until I knew I would be home.
And we hear all the time about people who neglected to check their configuration and found out later that they didn't order what they thought. Having to go in and re-do the entire vehicle order just for an accessory is not only time consuming but is prone to errors and possibly delays the vehicle you've waited so long for.
Putting these accessories all into one order with the vehicle also means they have to deal with partial fulfillment and tracking of backorders etc. from different parts of the company. All this change does is streamline things. Even with an established car maker, when you pick up your car your accessories are likely to be in the trunk (not installed) or they just walk back to the parts department and pull them off the shelf for you. In one case I had to schedule an appointment to install the cargo net I had purchased with the car (requires a special tool for the rivnut).
The only practical difference with this change is that you won't be able to finance your accessories as part of the vehicle purchase. If anything, Rivian might be losing a bit of money because of this since people might think twice about buying a fancy accessory if the cost is not hidden in the order total.
There is no "flip-flop" here or change in the "DEAL" you made with Rivian. And if you want to get technical about it, then you should READ that actual "deal" you signed in exchange for your $1000 - specificially Rivian IS NOT OBLIGATED TO SELL YOU A VEHICLE, and you are not obligated to buy. That's the "deal" - you can take it or leave it, the only guarantee Rivian gave you is that your $1000 is fully refundable.