It's not the same permit. Not only are there multiple levels of permits (Class A - high capacity, Class B - low capacity, FID - ammo and pepper spray), it is up to the discretion of your local police chief to implement any restrictions he might see fit. You may end up with a Class A, which allows you to purchase any gun available in MA but your chief may add a restriction of "Target and Sporting" which means that you can not carry concealed and should only be using your guns while hunting or at a range. The only way you can carry concealed is with a Class A and Restrictions: None.
Also, there is an appeals process if your local chief is a problem. It can be elevated to the head of the state police (forget the exact office) but I have no idea of the success rate. Luckily I live in a "green" town in MA where my local chief was more than willing to give me a permit, the local cops and I chatted while I was fingerprinted, and overall it was a pleasant experience. I believe they have the correct attitude that anybody who is going through the trouble to do this legally is going to be one of the last people they have to worry about.