1.What are people doing after 44B+K BE on block?
Its +2 on Block - what do you do after 11K on hit? You basically have 3 options:
1. JF Twister if you think they will press buttons.
2. Run up and throw them if you think they will stand still or try to step.
3. Run up and 1B:B them if you think they will crouch.
If you guess right, you will net 71 - 103 damage without clean hits assuming you know your combos. And this applies to any situation you are at + frames.
His low game isn't too stellar so what should someone do here?
Alpha has the highest output damage throws in this game save astaroth and then its competitive:
A+G, 8A+BB, 2A BE, JF Twister. = 97 dmg without clean hits
214B+G, JF Twister, JF Twister. = 103 dmg without clean hits
You dont need lows when you can output that much damage, mix the throws with safe mid launchers like 1B:B.
2. Does aPat really have a mid/low game? I feel this is aPat's one flaw. Most of his lows seem to be pretty easy to react to once you train yourself to see the animation. 11A, 11K, and even 1A

A all seem to have a pretty big windup.
He doesn't even need a low game, but as it happens - he has one: 1A: A: A is the only strong low you will really be using - RO to the right, almost 50 dmg, KND. Used sparsely this move connects, I've seen it at high level. And if your opponent can react to it, mix it up with B+K 62B 44B+K, because the two moves cannot be distinguished between on reaction. That's a low/mid mixup right there.
and instead just using his step killers and fish for counterhits?
Step killers? That's an area he is weak in and to be honest, you don't really need counterhits either, this character is all about throw/mid rushdown.
In this game, 1 throw + 1 1B:B + a couple of pokes = KO.