Well the modification rules do say you can remove any mod, even the ones that come stock on a weapon. Accessories also frequently follow slightly different rules than mods. Look at the silencer for example. The accessory gives a -4 to perception tests while the mod offers a -6. The sling accessory just makes it harder to drop the weapon while the mod offers concealability bonuses.
With the gas vent system I look at it this way. If I choose the accessory, I lose the barrel mount slot but none of my mod slots. If I choose the mod, I can keep the barrel mount accessory slot free but it uses up 2 of my mod slots. That is a pretty hefty price tag. The only things you are likely to use in the barrel mount accessory slot aside from gas vents is a silencer/suppressor or maybe a bayonet. There are all kinds of things you can use 2 mod slots for though, including other recoil systems. Having the accessory not removable balances that out and like I said, what else are you going to use the barrel mount for?
Keep in mind, in no way am I saying you can stack gas vent systems of any type. The rules are very specific on that one, but you can yank the gas vent mod, and only the mod, and replace it with a better system.