I would like to know how much difference in driveshaft yoke to transmission spline engagement is acceptable when not using a correct factory length driveshaft. In other words, if you wanted to use a driveshaft from a car that is a little shorter than the factory installed driveshaft that another car originally had, how much shorter can be considered adequate for engagement of the splines? Would a 1/4" shorter driveshaft be OK or would that be considered too much of a difference? The trans. is a 727 if it matters.

There are different length yokes so your question may not be easily answered. Trucks need longer yokes since their suspension travel is greater than it is with cars.
The general rule is to push the yoke in until it bottoms out, then pull it out between 1 inch and 1 1/2". That allows some "plunge" for when the suspension is in full compression moving the yoke into the transmission and enough spline engagement for when the suspension is extended.

I use the tranny yoke as a way to check for spline engagement by pushing it onto the tranny output shaft splines all the way so it is bottomed out and then pull it out 3/4 inch, this is with the car yokes that have 3.0 inch of spline inside them, not the over all length of the machined surface that slides into the rear tranny bushing in the output shaft
I make sure the car is at the weight it will have sitting still on the suspension on the ground and full tank of fuel to do this measurements

I like 5/8-3/4 back from butted, with the suspension loaded (not hanging free).

The "shove it in and pull it out X amount" won't work with the rear seal that has a dust boot.

Factory diagram below shows the preferred slip yoke position.

So, it looks like you should be able to measure from the axle yoke flat to the end of the tail housing and subtract

3.74" for the 727
3.58" for the 904

and have the drive shaft u-joint center to center dimension.

Yep.