I doubt that they will let people choose like that, since it would be extremely confusing to have two different varieties of Viewliner Roomettes available. It would also almost certainly result in cases of angry passengers getting the "toilet configuration" they don't want due to cars being bad-ordered.
What I really think makes the most sense here is to replace one Roomette with the two shared toilets like the V-IIs, but to still leave the en suite toilets in the other 11 Roomettes. That way, they don't have to go to the trouble during the overhaul of taking all the toilets out (which means the cars can be put back into service faster), all sleepers will have exactly 11 revenue Roomettes, and passengers riding in V-Is will have be able to use the bathroom in their room OR at the end of the hall. As to how they would now have to advertise the amenities of Roomettes since some will have the en suite and some won't, they could just leave it as a "surprise" to those who end up in a V-I, since those who don't like it can just use the one down the hall.