If the boot sector (first 16 sectors, i.e., 16 x 2,048 = 32,768 bytes) came from a Saturn ISO, then I think it should work. You have to keep in mind that the region coding of the boot sector you are patching must be compatible with the region of your Saturn console.
BTW, try to keep the total size of your ISO image (data + audio tracks) less than a certain time length, something like under 66 minutes... I'm not sure, but I do remember someone mentioning that Saturn games isn't supposed to exceed a certain length. To calculate the lengh of a mode1/2048 ISO file, divide its total file size by 153,600 bytes (i.e., 75 x 2,048 bytes) to give you how long in seconds, then divide by 60 to get minutes.