There is an old piece of advice in writing circles that says "slay your darlings". When a story has been worked and reworked many times, you will have created a number of great scenes, great characters, great plot lines, great emotional arcs, great endings. (At least they will seem great to you, they will be your darlings.) The thought of not using all these wonderful bits and pieces can seem intolerable.
In Story, Robert McKee describes this as one of the greatest impediments to writing a great story that works and sells. Rather than focusing on overall story structure, he says, rewriting becomes an exercise in trying to find new ways to include all of the "great scenes", the darlings, that you cannot bear to part with. But along this course things just get worse and worse as every iteration zigs and zags off the story course to incorporate the darlings. And often more darlings get created and added along the way, leading to a story that is full of great scenes but as a whole is an incoherent mess. Thus the ancient counsel: slay your darlings.
What you are proposing, to try to spare you darlings, is to turn your work into a novelty. There are a few novelty works out there, as Virginia points out. But novelties seldom sell well. And more to the point, novelties are remembered principally for their novelty. Unless it was you intent from the beginning to create a novelty book, then presumably you want it to be remembered for something other than this novelty. To get there, you need to slay your darlings.
Slaying your darlings is often very difficult. Sometimes the best way to do it is to put the work away in a drawer for a while. Pull it out in six months. By that time, you will have forgotten how much time and labour went into writing the darlings and it will be much easier to delete them. Also, you will probably find that it is suddenly plain to you which alternative is the stronger.
Don't worry at this point about whether you can do something else with the deleted scenes. Trying to make sure that everything gets used somehow is good hunter gatherer economics, but a poor artistic strategy. Give this one book all it needs, and only what it needs. Finish it. Publish it. Then go back to the scrap pile and see if anything there still so charms you that you have to spin it into another book. Don't worry if it is similar to what you have just published. If it is popular, people will be clamouring for another just like it.