I just tested the f1 into f3 and no, it's not a guaranteed follow up. You can always backdash or armor. Again, armoring out is very difficult since you can't buffer special moves while in hitstun. However, you can buffer a backdash while in hitstun, so that isn't hard. A delayed f3 will catch the non-invincible frames of some backdashes.
As for smoke's vortex, it seems to have the same weakness:
http://www.twitch.tv/gallopingghostarcade/v/79329386?t=01h36m16s
I don't know about the frame data involved, but Shady got blown up twice in that set and that time he even lost a bar on ex smoke bomb plus he ate a 27% combo.
If you want to get super technical, I suppose if Butcher's f1 hit on the last active frame, he could be plus enough to jail into a f3, but I'm not sure if that's even a realistic situation.