Fallout – ny non-aesthetic downside to salvaging everything in a settlement

No, because you don't have any skills/perks when leaving the vault.

You are prompted upon leaving if you which to change your Appearance or your S.P.E.C.I.A.L.

Points in S.P.E.C.I.A.L. unlock perks which also require points to use and upgrade.

You gain one point every level. So you build your perks as you level up, consult guides on how to choose your S.P.E.C.I.A.L. if you are going for specific perks/build out of the vault.

There's no known way to redistribute points after the initial prompt after leaving the vault.

However, using console commands on the PC version, you can set your perks and S.P.E.C.I.A.L. to anything you want:

• player.setav variable amount - set an actor value to a specific amount. variable can be a S.P.E.C.I.A.L., such as strength, intelligence or endurance. It can also be health, actionpoints for running attributes and skills, etc.
• player.modav variable amount - modify an actor value; the value will max out at its normal maximum value (100 for skills, 85 for resistances, 10 for S.P.E.C.I.A.L., etc.). A negative number lowers the variable.
• player.forceav variable amount - set a value
• player.advlevel - advance one level
• player.setlevel level - set level

Yes as the sneak factor of an armor is also determined by its weight-class. The heavier the armor, the less sneaky it is. You can also modify it to increase its stealth if the metal armor proves to be heavier.