I'm not sure it's down to the 4MB rom size as the MSI X58 Platinum SLI (MS-7522) also has a 4MB rom image and MMTool seems to work with it ok.
MMTool works fine with 4mb bios..MSI has used them for many moons, never had a problem... This is more an Aptio or hybrid UEFI issue...Not standard AMI bios most likely..