You can put a supercharger/turbo on a Mach 1, but you have to be careful of how much boost you put through it because like slowlx stated it has a high compression ratio, and the shortblock wasn't necessarily "meant" to have a power adder on it. But then again neither were the 5.0L fox body mustangs. You can do it but you have to be careful, and you cant really expect it to handle the same power as the Cobra.
As for the engines..... I don't know the exact specs off the top of my head, but the '03 Cobra has many more things done to it internally that makes it able to withstand the power of its supercharger. Ford assumed that people would modify it so they went to great lengths to make sure that motor could handle the extra power.
Although the Mach 1's engine isnt the same as the '03 Cobra engine it is almost (if no 100%) exactly the same as the previous model's Cobra engine. As far as i know the Mach 1's enigne is the '02 Cobra engine.