The tcase should be letting the front dshaft just free-wheel when its not engaged. And with the passenger axle in 2 pieces there shouldn't be any way for it to bind either. As long as the axle is separated and the tcase isnt in 4wd it shoudnt be any different than flat towing with an open diff.
I've never flat towed a yj so I don't know the proper tcase/tranny settings needed to keep it alive. My advice, post this question over in the YJ section. Substantially more active than this section, you'll get good info.
If you're wondering, the vacuum mod is a really failure prone item. It leaks and doesn't flex when it gets old. Either can keep you from having 4wd when its cold and/or you really want the front axle to work. Like when you're elk hunting, its fing cold, and getting dark and you're stuck on an ice covered climbing trail to get back to camp and you have no idea why you can't get the front axle to work. Just a f'erinstance.
The cable is a good fix. Or you go cheap like me and just run a long screw through it so the axle is always connected and the tcase just controlls 2/4wd.
I'm the only gay eskimo.