You have to look at it as if you were to play REO and how he would be responding to your set-up. Personally I feel that this makes me evolve my game play and strategies better and faster.
Even REO makes mistakes, but regardless of the wakeup properties of the attack, this is still a great strategy. Regular f3 and b3 are already great anti-wakeup tools because even if blocked, they leave you at +10, which is enough time to get off a f23, which is +9, which is enough time to get off a throw, d1, or cross-up. MB f3 and back 3 simply make the pressure totally safe. Even if your opponent uses an attack with wakeup invincibility, the damage is still solid, and your attack will recover faster than a lot of specials, leaving you at advantage regardless. Since not all attacks are actually invincible on wakeup, that also limits your opponent's options to the one or two moves they have that actually possess that invincibility.
F3 is my preferred anti-wakeup move because it hits overhead and leads to almost as much damage as b3, and I use it almost every time. This gets predictable. The opponent knows it's coming, yet because of the reasons I described above, there's just not anything they can do against it. At worst, they use a legitimate wakeup attack and we're left close to neutral, or they know to hold down the block button for the next 5 seconds of the fight and break my throw or block my cross-up, ending my pressure. Sure, some characters have tricks you need to watch out for, and some players might know a backdash trick or think to push-block you, but overall from a risk vs reward standpoint, it's an incredibly valid strategy, even against high-level players.
One last sidenote. Because the above strategy becomes so predictable, it becomes really easy to catch your opponent with a b1u2, which can lead to around 30%. b1u2 is totally safe because of the pushback, so it's really a matter of getting that 15-frame b1 to connect. You do have to be careful about overusing it because I hear the u2 can be stuffed if your opponent makes a good read, but otherwise it's good to toss out once your opponent starts to fear your f3 overhead.