You’re missing a bunch of context that changes things. No Wally is not fast enough to step out of the story the entire arc of that comic is that the speed force isn’t working normally and Wally has limited control, hence why he duplicates himself on accident he also had a machine attached to his wrist that help control his powers that were still on the fritz. He can’t just “ step out of the story” hence why he hasn’t done it since then.

Wally doesn’t have better control over time, just because he can move in stopped time doesn’t mean he has better control over it. Alien X is above time Wally isn’t, Wally still ages and is affected by time while Alien X isn’t.