Do the VATS perks like commando do anything outside of VATS?
No, VATS perks do absolutely nothing for you if you aren't using VATS. However, raising your critical chance is very helpful if you carry weapons with high crit % rates. So taking Finesse and having a high Luck is good to go that route. It gives you more crit hits:
To maximize this benefit I like to play an Unarmed/EW character. Then I carry Spiked Knuckles, the Deathclaw Gauntlet, a Laser Pistol and A3-21's PR which can take down Deathclaws and SentryBots with no problems. The great thing about Unarmed is you can use Paralyzing Palm when you get it at level 18 for Reavers and you aren't wasting ammo on them. Also, A3-21s PR if you run around can handle anything fast and if you use it sneaky can hit hard if you need it to for that first sneak crit, and when you don't get that first sneak crit, if you have raised your crit chance, then you get a lot of crits with it. Another good perk to take with that is Better Criticals which increases damage on crits. Although it requires high PE. There are small guns that have good crit % multipliers as well, that are also good out of VATS, like Blackhawk.
Here is a wiki link for reading about crit chance: http://fallout.wikia.com/wiki/Critical_chance
Here is thehttp://fallout.wikia.com/wiki/Fallout_3_weapons from the wiki so you can check out their crit chance rate if you want