Character choice

Your character choice mostly matters in Chapter 5 after you've been captured. Picking Rios saves 30+ seconds because his route is faster. On other chapters it doesn't really matter. The only other difference I've noticed is that Salem often spawns in front after loads or cutscenes.

Morality choices

Morality choices matter way more and optimal choices save over 1:30 across the entire run. Picking only bad morality choices loses only 2 seconds compared to optimal while only good choices loses a lot of time.

• Chapter 1: execute. Saves around 17 seconds.
• Chapter 2: return weapons. Saves around 2 seconds.
• Chapter 3: execute. Saves around 26 seconds.
• Chapter 4: get sniper rifle. Saves over 30 seconds. This one is a bit more complex because it changes multiple sections but overall getting the sniper is faster. It skips some extra dialogue with the kid after killing the flamethrowers.
• Chapter 5: take bribe. Saves around 17 seconds.