metal channel location for door/quarter window upper seal

[femtnmax]

The channel that holds the "top" seal for door and quarter window, at the back where the channel stops near the lower aft corner of the qtr window....should the outside lip of the metal channel line up with the horizontal quarter window seal where the qtr seal attaches to the quarter panel?  There's a thin chrome? strip that the qtr seal has on it where the seal attaches to the qtr panel.  I lined up the thin chrome strip with the outer lip of the roofs metal window channel as shown in the photo.
The problem I have is the unibody assembly just aft of the qtr windows is not the same drivers/pass.  The passenger side had many missing spot welds and the interior metal structure was not lined up even close to what was done on the drivers side.
I have a pic of the drivers side, wondering if this looks correct, then I can make the pass side the same.

[Bullitt-]

My car is unmolested in this area, my passenger side looks like your picture but the drivers side the channel is outboard a little in the area where the offset is in the quarter panel.
 In both cases the glass pinches the seal about the same amount so some adjustment may be necessary for best seal. I've never messed with it yet so this is just a guess.

[femtnmax]

the drivers side the channel is outboard a little in the area where the offset is in the quarter panel.

Would you say the channel is outboard the width of the channel flange, less, more? thanks

[Bullitt-]

It would be about the width of the flange, my felts are off so there is nothing to judge it by, but you can see how it fills in the notch

[femtnmax]

Good, I'll try and match that. I wondered what to do about that notch. I installed the felts with RTV behind them to try and reduce leaks.  Maybe I'm just kidding myself. Thanks.