I don't think there's any need to present an alternate cut of the battle sequences or indeed anything else (including alternate audio). Don't worry about that. Make one good cut. (Although do put the alternate apocalyptic ending on there!)
The Sci-Fi cut is worth preserving by itself, unmodified and exactly as it is - I also have it on VHS somewhere, an old showing with a different watermark.
Just slap the Sci-Fi cut onto a different DVD and call it a day.
I'm amused by some of the Bruce Campbell lines used to cover profanity in the Sci-fi cut ... "I ain't never even seen these apeheads before!"