I aint Rhubarb so maybe only he can answer exactly. But I am making a guess here that it really doesn't matter if you go for DS3615XS or DS3617XS because you need to create a new usb drive to boot the DSM 6.1 or later iteration anyway. Moreover latest Jun's loader for DS3615XS is v1.02a whereas the latest is v1.02a2 for DS3617XS, which is a later revised version. Although I remember v1.02a2 only contains very minor change, it still make sense to go for the later version if you were to try something new.
Having said all above, neither of the two loader work for my setup with both error 13, which really is a bomber.
1. jun's loader v1.02.a2 is a fixed loader for ds3617xs, v1.02a has "time bomb"
2. ds3617xs is compiled for new cpu architecture, with new set of instructions, hardware acceleration etc. if you use it on old cpu then it can cause problems on some part of dsm and packages, but users will blame xpeno loaders. for sake of safety and peace of mind its highly recommended to use emulation of ds3615xs