Whether or not you find Gareth at the abandoned house depends on a timer that starts ticking when you leave The Lady Vengeance for the first time, if you take too long to get there then you won't find Gareth in said house, even if you stop by the house before reaching his home.

This quest is messed up. I approach his parents house and I see him first time there digging his parents grave. I agree to find murderer. I found gloves and I follow the trail. Later on I think I killed the guy. After some time I go back to Gareth and he still digging and don't want to talk with me. Saying those silent monks killed his parents. So I need to enter there. I dispatch paladins guarding house with pesuasion. I enter and Gareth wants to kill them all. Im like no dude, wtf, I got the guy who did this. I got his gloves and all but theres no such option to tell him about it. So I manage to calm him down and he appologized and went back to ship.

And now I reading I could prevent his parents die? How, where, when? There was attack of voidwoken there? When? Messed up.

I in the first place completed all the quests in the Blackpits area before ever entering Paradise Downs, and met lots of bugs in this quest:
1. Gareth was nowhere to find. I checked every place possible.
2. Only when I broke into the farmhouse in Paradise Downs, Gareth appeared from nowhere (maybe he truely masters the arts of void).
3. Then I chose to kill Jonathan in the dialogue with Gareth, but J was already killed during the fight rescuing Hannag's apprentice. AND THE QUEST PERMANENTLY STUCK HERE, AT THE REQUEST TO KILL GODDAMN JONATHAN.
*I have never seen the scene of G and J meeting, or G digging in front of the house. The whole quest is a mess.

!!!WARNING!!!
This quest determines how Gareth will interact with you in Act 3, Act 4 and end game.
For the best path, Gareth will lead your crew on Lady Vengeance and pray for your victory before the final battle.
For the worst path, Gareth will become a Silent Monk and fight you in end game.

For the best path:
1. Convince him to kill Jonathan
2. Defend Gareth's parent from Voidwokens
3. Talk Gareth down when confronting Magisters in Act 4.

For the worst path:
1. Convince him to spare Jonathan
2. Help Gareth to take revenge on Jonathan
3. Help Gareth defeat Magisters in Act 4

The best path will grant you about +70000 more XP in a grand total, but you won't get a +1 Thievery unique dagger. Your choice.

I did this quest both ways. In the option where I find Gareth in the burning house & convince him to kill Jonathan I had the option later on in the Nameless Island to side with him against Alexandar, BUT, then he's all sullen and brooding on the LV and, at the last fight, one of the big bosses - not sure who did it - Lucian or Vredeman, brings him into the fight against me! - he got owned pretty fast but still, what was he doing there? Isbeil, Kemm, etc. were revived from dead, but Gareth was still on the ship, very much alive and supposedly on our side, when I went into the cathedral...

In the other version where I find him burying his parents, I had picked up Jonathan's gloves before I talked to him, maybe that's why, when I went into the house he rushed in behind me and demanded that I kill the silent monks. In the first option I agreed to 'take care of the monks' and then he rifles the house to find evidence who gave the order, doesn't offer any other dialog options to give him the gloves as proof or tell him that his parents ghosts told me it was Jonathan. In the option where I persuade him not to kill the monks I got something like 6K xp and he left for LV (where he's tormented by sorrow & demons and can't talk to me he says).

The encounter with Gareth and Jonathon is not on a timer, it gets triggered if you go anywhere close to the house, and will disappear if you leave the area without doing the encounter.

is there a mod that allows you to save gareth's parents after having visited stonegarden? i really want them to live

I stole Jonathan's ring while he was unconscious at the burning house and convince Gareth to let him live. Afterwards in the farmhouse, once i had kill the monks and got the instruction to find and kill Jonathan, i just gave the ring to Gareth without even leaving the house. The quest ended in that moment.

I see no indication the game recognizes that Jonathan is still alive. Not sure if this was intended to be an option but i guess it works. The quest shows now as closed.

Location of Jonathan's Gloves: (X:692, Y:277)

The gloves can be difficult to see. On PC you can hold the "Alt" key to better view items on screen. (I'm assuming there's a way to do this on consoles too.) Change the mini-map so north is facing the top. Head directly to the east of Gareth's family farmhouse. The gloves are located southeast of the tree, where the fence ends. They are in between the fenced and the small rocky bluff. To be clear to the point of over-clarifying, the tree is the nearest tree to the farmhouse that is both south and east of it.

Does going anywhere near the stonegarden waypoint make this quest fall into the "Jonathan Lives" branch? I didn't even reach paradise downs and i couldn't find gareth and jonathan at the burning house lol.