Most of Toyota's profit comes from just a few best selling models (that tend to be their best selling models year after year). That's where you'd start on this type of automation, and you'd invent new manufacturing technology accordingly as necessary.
The criticism I see most often on the concept, is that it'd be challenging because our manufacturing processes are pathetically ancient. I agree: it's time to move manufacturing into the future. It's not a question of if it can be done, it's: who is going to do it first.
The actual integration part isn't the problem, I don't believe. The dealers themselves could probably do that with a little help and some changes if you could deliver them a crate of all the parts. When you buy a Honda accord, there are at least 3 different power train options, a 4-cylinder manual (do they still make this?,) a 4-cylinder CVT, and a 6-cylinder automatic; and Honda has been amazing at actually reducing the number of options over the years. Do you build the power train on demand or do you attempt to forecast sales and stock an inventory? That's a very significant part of the overall cost. Many of those parts are forged and then machined both, just building the head takes some time and precision, let alone assembling it... there are interior changes that have to integrated as well, from the dash display to things like paddles for shifting in some formats.
With a lot of modern cars, I wouldn't be surprised if the rolling chassis for the different models is very nearly the same but subtly different depending upon the power train. Toyota has the highlander, it's a very popular platform, it also comes in a hybrid configuration, I suspect that are more than just some subtle changes to a lot more parts for that. Same with like an all-wheel drive as an option type products... or convertible roof. I think the navi-option on some mass market cars results in a different dashboard molding.
If you limit "options" to color and seat materials, this is an easy problem. The auto industry practically invented options though, like Ford and Lincoln and Mercury were the same vehicles for a long time, the fake options helped sell way more product. Today when you buy a Camry, it's almost like there are four or five entirely different products that are all labeled "Camry" from like an entry level spartan 4-cylinder edition up to the hybrid limited that costs nearly twice as much. The market seems to like that. That's the trick, if you could some how convince the buyer that they had real options but they didn't... Maybe electric motors are a big part of that, take performance off the table as an option and things can be made more simple.