I think RAT trannys only came behind V8's in broncos. RAN and HEFs came behind either engine but my interchange manual could be wrong but bottom line is that case ID wont nessarily tell you the gear ratio it has. Basically you need the short output shaft version for 6cyl application it will have the lower gear in it. Not sure on the exact lenghts of the ooutput shafts but the 6 cyl version should be close to 6in while the V8 version is closer to 9in.
And yes you want the lower geared version for a 6cyl they need the extra gear as they dont have as much torque on take off thats also why 6cyl vehicles tend to come with lower axle gearing as well.
The stock 3 sp gearing leaves a lot to be desired so I'd definitely want the lowest gearing I could get.