It must be an absolute pain, with an issue like this.
As the risk of stating the obvious
Have you checked the recessed roof Chanels to see if :
A) the plastic end cap are seated correctly
B) all the fixings (rivets) are present and correct (in the channel)
With the roof up are all the fixings in the body panel ( especially at the front sides of the roof where the roof seal meets the fixed bodywork) correctly sealed with factory mastic type material ? Should be a thin white film over all fixed parts.
Agree with the paper pinch method for checking the seal,
The seal(s) should grip the paper otherwise it is not sealing fully.
The front lower seal looks like it’s being depressed.(compressed)
The front mesh window like like it quite wet ?
Is the top seal seated properly on the front leading edge of the roof?
I recently had a roof seal replaced, the dealer fitted under warranty, however they did not fit the inner skirt part of the seal correctly to the front curved profiles ( both sides near the edge of the roof) if water had passed through the top (upper) part of the seal where it grips the roof panel, it would have been able to get inside the roof area, a little tweaking of the rubber seal curves sorted it, although it would have to be fairly severe IMO to let a volume of water pass.
Is the canvas skirt seated properly at the bottom and top plastic seal that attaches the canvas to the roof panel and fixed part of the van, I have seen these pull out ?
Do you park on a relatively level surface ? Ie do you park on a slope nose down ?
You mention that the dealer “repaired” a damaged roof drain ? Did they take out the headlining to replace the entire tube ? What did the repair entail ?
The fact that the water appears be above the headlining in the raised roof section would probably discount an issue with the drain tubes themselves (which if faulty would allow water water to back up in the channels and overflow into the cab headlining area, therefore I would suggest checking everything above that level or backwards from that point to ensure everything is sealed, over the entire roof length.
Can you remove the comfort light in the elevating head lining (seen in photo 5 of your first post) and see if there is evidence of water / moisture in the void / on the back of the lamp/ wires etc.
Is the elevated roof lining damp at the back after the roof has been raised for a period of time ?
all of the above sounds obvious I know, but just trying to prompt lateral thinking to discount certain things and identify possible areas where the issue may be occurring.
More questions that Answers, but I hope it give you a few additional thing to check and discount.
May be worth asking
@VW Guru for his thoughts ( top man and VW Cali master Tech)