Made a note, this sounds like a bug, yeah. The salvage bonus does not - or at least should not - affect the weapon drops, and it should *definitely* not change them.
I'd rather there be a way for the player to change what Omega weapons actually drop, instead of having the drops be effectively locked on game creation. Since the player won't want to get through a playthrough to the point of fighting the Doritos only to find out that the drops are useless ones, and then deal with that for the entire playthrough. Right now the larges are locked on game creation but the mediums and smalls can be changed by changing the fleet's salvage %, and the only way to otherwise change what Omega weapons you get is by rerolling the unique bounty.
If the design purpose is to limit the number of Omega weapons that the player can get, then a solution would be for the Doritos to drop a certain number of "weapon blanks" that the player can then trade in at some contact or machine or whatever to choose the Omega weapons that the player wants. This way it's still limited, but the player won't be stuck with a bunch of undesirable weapons.