As long as the modification can be reversed, I don't see a problem making the mod. I would take a bunch of good pictures before the mods, kept in-case you sell. You could then show both variations as a selling feature. Give your buyer a choice, couch or captain seats.
In my particular case, I cannot see anyone ever thinking that barrel chair is preferred over the third captain seat. I hope to sell the barrel chair, just to get it out of the house and recoupe $100.
If I was worried about resale, I would have included the slide-out option in our order. But then the motor home wouldn't be what we wanted.
When selling any vehicle in general, if it does not look "owner modified", with good presentation, you should be successful. I had a hobby of buying and selling Corvettes. To be successful in getting the car's true value, it must look like it just came off the factory floor. Internet pictures must be of high quality, showing every detail with proper lighting and all the rest. Good pictures and good description will get the inquiries and eventually will make the sale happen.
It makes me smile when I see a used motor home for sale by owner with everything personal still inside the thing showing how "lived in" it is. That is NOT good. They really need to get 100% of their personal stuff out, clean it all up well, close the cabinet doors, fluff up the couch bolsters, open the blinds, lower the toilet seat, etc. etc. then take great pictures. If they want to include personal stuff, place it all elsewhere, take pictures of it separately, and keep it all separate, especially when people come to see the motor home in person. The goal is to make the buyer feel like they are buying a "Like New" motor home.