Thinking about it, the MT6 Maguras I have had a similar problem.
The solution I found was use the standard bleed block and do a bleed, except when the bleed is good, remove the bleed block, mount the caliper on the bike with pads, pop the wheel in, then open the caliper port and push an additional amount of fluid in to close the gap between pad and rotor, close the port, remove the wheel and pads then tidy up.
Thinking about it, the MT6 Maguras I have had a similar problem.
The solution I found was use the standard bleed block and do a bleed, except when the bleed is good, remove the bleed block, mount the caliper on the bike with pads, pop the wheel in, then open the caliper port and push an additional amount of fluid in to close the gap between pad and rotor, close the port, remove the wheel and pads then tidy up.