If you read the various articles on updating Myford ML7s from narrow to wide shear location, you will see pictures showing that in many cases, of used machines, the saddle does not make overall contact with the bed. In which case, it could be liable to wobble in a vertical plane.
Also, to enable the saddle to move along the bed, it must have clearance.
So if there is any clearance between saddle and bed, there is the chance that it it may change (very likely if the bed is twisted ) and so introduce inaccuracy.
Laying the level so that it rests on the bed minimises the number of parts involved and sources of error.
The more directly that the measurement can be taken reduces possible errors.
Not applicable in this case, but think in terms of drilling ten holes in a strip of steel, with Centre distance 1.000.
If you dimension every hole from one datum point, then every hole will be within 0.005" of the nominal position.
Dimension to a +/- 0.005" tolerance on the individual centres, and the last hole one could be as much as 0.045" more or less than the nominal 10 inches.
The moral is: minimise the number of dimensions involved. So work direct off the bed, because that is what you wish to measure, not in terms of thous or microns, but graduations on the level..
You would not try to measure the backlash in your cars transmission by measuring an angular movement between the road wheel and the flywheel
If you did, there will be clearances in both ends of the drive shaft, gears in the differential, gears and their splined shafts, gear to gear clearances, and between the splines between first motion shaft and clutch centre plate.
But you would not know if there was an excessive clearance at any one point..
As the amateur radio fraternity say, KISS "Keep It Simple Stupid"
As an Engineer in a Quality Department, I was trained to think logically, and to measure as directly as possible.
Howard.