I don't think the master cylinders are going to be the same for the GT350 and Mach 1 but I can hopefully tell you the external piston size of a GT350 master cylinder in a week or so. I am working on a similar plan on my 2015 Performance Package GT myself. My plan is to keep the front 15" GT Brembo brakes and add the rear 15" GT350 brakes. I am going to use GT350 rear control arms, knuckles, parking brake, hubs, calipers, cables, bracket, ect. I also have a GT350 master cylinder coming too. Based on my research and calculations the 6-piston Performance Pack GT, Bullitt, and Mach 1 front calipers and 6-piston GT350 front calipers have almost the same piston surface area; 3054 sq mm based on 34mm/36mm/38mm pistons in the GT350 caliper compared to 3052 sq mm based on 36mm/36mm/36mm pistons in the Performance Pack GT, Bullitt, and Mach 1 caliper. I have seen conflicting sizes listed for the GT350 4-piston rear calipers; 30mm/32mm pistons and 30mm/30mm pistons. Either way that is a huge increase in the piston surface are for the rear brakes at either 3019 sq mm or 2826 sq mm compared to 1554 sq mm for 44.5mm piston in the GT, Performance Pack GT, and Mach 1. I have seen threads where multiple people have upgraded their Performance Pack GTs using the M-2300-Y kit you referenced. They all appeared to keep their factory Performance Pack GT master cylinders and said they could feel an increase in braking performance. It appears a base GT has an external master cylinder piston size of 27mm and a Performance Pack GT/Bullitt, Mach 1 is 28.5mm. I haven't seen anything mentioned about a staggered inner bore but I think that may be the case. That would be one way Ford handles front to rear brake bias. The base GT and Performance Pack EcoBoost cars both use the same 4-piston front calipers that actually have a much larger piston surface area at 6500 sq mm for the 45.5mm/45.5mm pistons and use the smaller 27mm master cylinder. Maybe I can get a look at the inside of the GT350 master cylinder by throwing it in our x-ray machine.
Remember, the stock GT rear caliper is a sliding caliper and the 4 piston models fix the caliper in place. Because of this, when you compare the two, you need to double the piston area of the sliding caliper for an apples/apples comparison. That 30/32 combo of 3019 sq mm is very close to the 3108 sq mm of effective area for the standard GT (+3%).