Sorry I have not been around to catch results from your investigation.
Are the rust spots under neath the rubber seal or starting from the roof going to the seal?
It could be a stone chip that has not been treated.
I know my window screen is bonded into place and the rubber is only a kind of trim that fits into some clips. If you go down If you are going down the route of windscreen replacement you will
have to ask the window screen fitter to wait awhile as the screen is bonded into place. They may not be willing to wait. But you never know until you ask. Once the sealant is on the glass there is only a certain time to fit it.
As Miggy said you could try the leak seal treatment. Could also look at the inner seal around the sun roof. Pleased that the drains are clear.
DaveL