I've never made two port wines simultaneously but feel confident to say port batches can turn out differently, due for example to chaptalization variances. (It's possible to work with alcohol content and sweetness.) I think it would be interesting to make them individually and decide later what you want to do. You can blend them together later or adjust the flavor of each.
I just made my first CRP and it came out great, but with all the issues everyone has reported, I might try them as individual kits to control the issues more easily if they arise. Possibly blend them at bottling time.
Someone with more experience may say the a single 6 gallon batch is a walk in the park.