I liked those Yamaha brakes around the 250/400 DX time. They seemed to be less conservative with the ratios they used compered to the other makes and had a mix of light touch with power and feel that was a really good balance.
Going back to the leverage. If you first strip out the brake lever and just look at the hydraulic section it makes it easier to see what's happening. If you extended the piston to the same area of the calipers (extreme for illustration purposes) then you have no ratio advantage at all, and probably wouldn't be able to get any appreciable force on the brake pads, this would be a 1 to 1 ratio. Then you leave the calipers alone and keep reducing the bore of the mastercylinder to a point at which you have the ratio advantage you want. This shows that by reducing the mastercylinder bore you create a ratio that trades movement against leverage, so better able to pressure the pads but you now have to move the mastercylinder piston further to achieve it. In other words a mechanical advantage.
Then you add the lever back into the mix. If you measure the distance from lever pivot point to centre of piston and compare it too the lever length, it will give you another ratio that will act as a multiplier on top of the hydraulic one.
So depending on the area of the caliper's pistons, if you use a mastercylinder of (obvious used range) between 10/16mm to get a ratio you want then manipulate that total with a different lever ratio, you end up being able to produce a similar brake line pressure but with different "feel" to the lever.
The newer radial type mastercylinder seems to go for lower end bore size (as Trigger mentioned) to get the most potent hydraulic advantage but then use a variable/ adjustable lever fulcrum ratio to alter feel for rider preference.
The screw on those old Yamaha levers just moved the lever to accommodate differing hand sizes and not the ratio. If you move your hand out to the end of the lever you do increase the leverage though, compared to using your two principle fingers nearest to the pivot point.