The reason is encouraged mainly by costs, 1 car is cheaper than 2. Very few example at a professional level exist due to the reason you stated, but why not have a base car that you can then just adapt to one discipline with your necessary parts bin. Then when your done with it, you can 'bolt on' a different package and enter the same car in another discipline. You can then have some technology cross overs that might actually have a benefit.

Alternatively anyone wanting to buy your car off you won't be restricted to that discipline.

Then using this approach maybe take it a step further - if you know what's required to turn a DS3 rally car into a DS3 Rally Cross car, why not take on the challenge to make the necessary modifications back and forth as your entering it across the disciplines. You can still fine tune the said car for each track/stage as well for optimised performance.

While I agree with you, however each car can still be open for competition and optimised for each track. Regulations hold a big restriction here with crossing over disciplines but if things like roll cages and safety equipment can be generalised then why not!