I think Al probably guards Simmons.
If they put Semi on Simmons instead, they probably have to go small - put Al at the 5 guarding Embiid. I think they want to avoid doing that for long stretches - Embiid is a big dude, and although he does drift out to shoot the 3, he also likes to play physical near the basket. Al has said he doesn't love playing true 5s, and it's not where he's at his best.
If you have Baynes on Embiid, that might match alright for us defensively; Embiid will encounter a willing, physical defender, and Boston should be able to bring spot help. Embiid might even be a little more tempted to shoot 3s - which is definitely where I'd rather see him. When we have the ball, if Semi is in and Baynes is out, you might see Embiid playing way off him the way Giannis did - clogging the paint and creating a real problem for us. Giannis is a tall, athletic player, but he's not as good a defender as Embiid. If Embiid is free to play center field he could be a real menace on defense.
But I'm sure there will be some experimentation. Certainly when Embiid is out there's more room for different things to happen. And the way this season is going, we might see all kinds of crazy lines out of necessity.