I might first look for another Alpha six-speed, though those are not terribly common. They turn up on a fair number of late-'80's mtb's.

I feel that a Shimano six-speed UG or HG freewheel is the way to go here. Better shifting teeth, and these have 3.6mm cog spacers with 1.9mm cogs, so identical to Suntour's 5.5mm Accu-6 spacing.

Never flip the cogs on a Suntour freewheel. The teeth are not symmetrical, and shifting will be terrible at best. I have come across this trick after a rider brought his non-shifting bike in for service. The funny thing was that the cogs didn't even have a wear problem to begin with, so at least was easy to fix, once the problem was diagnosed...

I often ride briefly cross-chained in the big-big, but wouldn't ride in the smallest sprockets crossed over.
The chain will be slapping the chainstay, removing paint, and the stresses and wear rate over the smallest sprockets will wear them out much faster as they have fewer teeth.