If it's only 1/4" difference, doesn't matter where you measure from, but I measure from the blades. Just a couple of helpful tips from an amateur operator:
First, deck angle on the RC should be determined by a couple of factors.
First, if you have really tall/thick material to cut (like the first cut on an overgrown property), it is generally better to have the front of the deck angled slightly down, so as not to be cutting the same material twice and bog down the machine. However, in my experience, this tends to leave clumps of cut material and looks bad. If you are cutting really tall/thick material, it's probably just not going to look that good after the first cut.
Angling the front of the deck up, lets the blades cut the material twice and mulch it up and also tends to leave it more evenly dispersed and with less clumping. Maybe if you have a high-horsepower machine, it doesn't matter and you can just run with the front of the deck high anytime, but I only have 21 PTO HP, so it is a consideration for me.
Second, you need to just experiment with the adjustments to see the best way to get the cut quality and final cut height you want. The way I do it is set the deck angle for the cut quality, i.e., do I want front rake for rough cut or do I want rear rake for more finished look. Then, I use the three-point lever to set the lowest point of the blades, measured from the ground, to get the height of cut I want. Then, I adjust the tail wheel as necessary to hold the desired cut height.
Finally, I keep a notebook with several settings listed that I can refer to depending on cut height, etc. The settings in the book are: cut height, tail wheel setting (i.e. which bolt holes are used in the adjustment), the number showing on the rockshaft (three-point) lever, and the number of threads showing on the top link (measured with a tape measure) so that I can refer to that dimension to set it the next time.
Sounds complicated, but since I only cut the same pasture the same height every time I mow, I have gotten it down now to the point where I always use the same settings so all I have to do is refer to the top link setting and re-adjust that. The tail wheel and rock shaft lever settings stay the same.
The only reason I have to change the top link setting is because it is different from the setting I normally use for my finish mower which is normally on the tractor.
Hopefully, this makes some sense. Maybe the old pros on here have some better ideas, but this is the method I settled on.