The only major downsides in my opinion are if you try to do the hold volume up+home+power button to get to recovery (or is it volume down? I forget...), you go straight to the stock recovery instead of Safestrap. Also, if you don't hit the button to boot into Safestrap in time you have to wait for the phone to finish booting, turn it off, and try again. You can't flash kernels with it either, but that's not Safestrap's fault.
It has its upsides as well. You get several slots for flashing ROMs and mods so you can run several different ROMs at the same time without having to wipe out your phone to try a new ROM. Each ROM you flash has to be based off the same version of android, though. That means no Fire Note in the stock slot, Dynamic KitKat in the first, S5 experience in the second, etc. There's more discussion about that in the Safestrap thread.