A ruleset so that precisely outcomes like these, which satisfy no-one, don't occur.
The only time you will see two opponents pitted together like this is when there is a tremendous money put up on the line from one group that is desperate to get attention.
There won't be neutral rules when one side has way more on the line than the other.
Ali was the "A side. " He simply says "no" and the match/exhibition/whatever you want to call it falls apart. The mere fact that New Japan Pro Wrestling had to go outside of their own circle to get something like this done with the top earner in another sport, turns all the power over to that opponent. In the end, even though the match stunk, Inoki became a name over in America (which was the objective) and in time, fans forgot how bad the match was until the Internet age. Inoki raised his profile on the world stage. Money well spent once the stink went away.
NJPW is lucky that Inoki was a business man and didn't walk out on them as the original concept pitched to him was by Vince McMahon Jr. When Ali went to Japan he found out it was a shoot (real match) and not pro wrestling. But Ali compromised enough for the event to go forward.
Ali lost a lot by agreeing to do anything but boxing. "The Greatest," was never the same after his match with Inoki due to the blood clots that developed in his legs from all the crab kicks. his reputation took a hit as well.
More A side stuff: It was rumored to be more of the same situation when Frank Shamrock wanted to face Mike Tyson. It was Tyson's rules or nothing. We're seeing the same thing with RIZIN and Mayweather. It won't happen any other way. There is some money to gain from the A-side, but there is also the potential hit to their reputation for taking on such a contest under mixed rules. A damaged reputation hurts future earnings.
Now if we're talking two unknowns going against each other, one from boxing and one from grappling/MMA, you'd have to convince an athletic commission to sanction it for starters. Those crusty, corrupt groups take forever to come around to anything new or different. They would simply say it would likely have to be contested under MMA rules.
Once the you get two mixed fighters to agree to compete, would it be approved?
I went to Vegas for the first PRIDE event "Real Deal." Mark Hunt who only had a handful of MMA bouts was scheduled to face Butterbean. Both of these guys were seasoned combat sportsmen. Hunt more from kickboxing than MMA. Butterbean from boxing. The athletic commission wouldn't allow them to fight because Butterbean was deemed too inexperienced in MMA. The same commission approves 49-0 Floyd Mayweather Jr. to fight 0-0 Conor McGregor in boxing. This is an example of only seeing the big money earners being worth the corrupt athletic commission to turn a blind eye to the lack of experience of a fighter in a given sport.
Maybe in Japan and other countries where there are no commissions or they have a different perspective on competition or really want any sort of revenue, they'd allow what you are proposing. But you're only going to get no-names doing this sort of bout. The closest to mixed-fight rules that isn't MMA, that has next to no following is Ganryujima. It doesn't count on an MMA record, but it is mixed martial arts.