If I migrate content of an old MacBook Pro to new one, will it also transfer the file folders created in Mail?

That's my understanding, assuming that you selected the options to transfer everything. It is important to carefully rad and understand the options you select. You do not have the option to be selective about transferring some of your files. It is all or none.The same is true for your apps. Understand that if you have some older 32 bit apps installed in the old computer, they will not work in the new 64 bit computer, and they will have to be reinstalled to update them.