I'm still trying to figure out what Trion's plan is with synergies, but I've now gotten a number of synergy situations to work, so I thought I'd pass on what I know.
1) Starting origin doesn't mean anything.
2) There are two synergy systems:
2a) The weapons with just a benefit for , mean that if you equip 2 weapons of that synergy type in the same loadout, you receive the bonus. (Survivalist, Machinist, Veteran, Outlaw... and probably Wrecker, Hard-Boiled, Nano-Executioner, Nano-Mastery, and Sawbones although I haven't tested the last five).
Example: A sniper Rifle with Survivalist does 1271 normal damage and 4386 normal crit on uninjured foes. I equip a stowed Survivalist pistol as my secondary weapon in that loadout and the sniper rifle still does 1271 on a normal hit... but now does 4605 normal crit on an uninjured foe (the description of Survivalist says 2% damage, but it's actually 5% extra crit damage at the time I'm writing this).
That explains why we aren't seeing any mods of the above synergy types.
2b) The weapons with synergies that have ,,, bonuses listed mean that the weapon will accept those types of synergy mods and recognize those synergy bonuses. Assassin, Brutal, Cannoneer, EGO-Precision, Prepared, Quartermaster, Rolling Thunder, Run-n-Gun, Scavenger and Stalker.
Example: The Crystal Pond triggered vendor sells a Brutal synergy Frontier Shotgun. If I place Brutal mods in a Brutal shotgun, I get the listed bonuses... one tier per mod.
The gun does not appear to have an inherent level of the synergy, it just recognizes mods of that synergy if you use them. You don't get one level of Brutal just from an empty shotgun. You don't get any levels of Brutal from equipping two Brutal shotguns without mods. You don't get ANY levels of Brutal by putting Brutal mods in non-Brutal weapons.
So it seems very limited to adding Brutal mods to a Brutal gun... with the number of mods equaling the level of bonuses received for the weapon that is drawn.
I haven't heard of anyone getting actual mods for many of the -level tiers yet. You can buy EGO-Precision, Prepared, and Scavenger guns and mod caches for reputation at faction vendors after EGO 250 unlocks Factions. Most people are getting a lot of Brutal and the occasional Run-n-Gun from the keycode Synergy Mod Caches.
One hypothesis is that Assassin, Cannoneer, Quartermaster, Rolling Thunder, and Stalker synergy mods may not start showing up in Synergy Mod Caches and Vendor Specials until very high (end-game) EGO ratings.
Anyway, due to character wipes... I think a lot of the synergy system came into launch poorly tested... so it's taking a while to figure it out. But that's the best I have so far.