I served two tours (eight+ years in the Marines) and was a police officer for fifteen. So this is my opinion and only my opinion on firearms familiarity.
To me, if an untrained person picks up a weapon then changes to a different weapon of the same type, they may have difficulty operating it correctly or how to correct a malfunction. This is just from not knowing firearms in general.
However, you take someone who has been trained or has used a particular firearm for some time; months or years... they are going to understand how most firearms operate and would be able to operate a foreign weapon to them and even be able to correct battle field malfunctions (immediate and remedial actions for most weapon types are usually the same). As for using a weapon, different weapons have different factors that change how someone fires them; trigger pull weight, recoil and anti-recoil systems, weight of the weapon and where that weight is on the weapon... so sure you could impose a penalty for not being familiar with a weapon platform.
With that being said, if you are just imposing a -1, that doesn't seem unreasonable to me for picking up a weapon your character is not familiar with. But on the flip side, not imposing a penalty and using the rules as written wouldn't seem out of place to me either as firearms of a type are fundamentally the same. Just a matter of what a GM and/or players feel should be the case. Kinda like house rules; vast majority of games don't need house rules but some people feel the need to add anywhere from a few house rules or to add hundreds of house rules, it is just a GMs take on what works and doesn't and how they want their game. Neither way is wrong or better, just personal choice.
Just my two cents,
Oh, and on the topic of zeroing a weapon with adjustable sights... When you properly zero a weapon with adjustable sights, you are zeroing it for you and you alone. This doesn't mean that someone else cannot pick up your weapon and not hit a target. Just means that all things being equal, his rounds are going to strike slightly off from where your rounds are going to strike and sometimes this means off target. Boresighting is different than zeroing a weapon.
And to give an example; when I served... my Gunny wanted a fellow Marine (my security element) and myself to zero each others M16A4s, just in case we had to pick up the others weapon and use it. Both weapons only had iron sights, both adjustable. When he zeroed his M16A4, he was flush on the front sight, and had three clicks right. But when I zeroed the exact same rifle I had to go two clicks down on his front sight post and thirteen clicks left on the rear. And then for my own M16A4 I was flush on the front and seven left on the rear... when he zeroed my rifle, he was flush on the front and zero clicks (centered) on the rear. Go figure. LOL
~ Not as lean, or as mean, but always a Marine
~ Go with God, but make him walk point.