Frequently, I find that the roof is slightly damp in the morning (dew/melted frost etc.) - I have never had a problem with stowing the roof in this condition.
This is the second convertible Saab I've had (the other being a 900 SE Turbo) and no problems with either, as far as using slightly damp roofs.
Having said that - my cars live outside, and so the roofs naturally fade a little over time anyway, so maybe the 'white marks' if any, are less noticeable.
The black roof I had on my previous car, I re-proofed and coloured using Renovo from PFS. I have some blue Renovo for this roof, but have not yet used it (the car is just over 3 years old now)
Oh, just remembered that I did have a bit of 'mould'/mildew in the stowage compartment of my previous car. I found that half-opening the roof, so the 'lid' was up and the stowage area exposed on a hot summers day allowed both effective cleaning and drying of the area - resulting in no repetition of the mould issue.
If it's dry weather - the roof is down, unless I have my larger suitcase in the boot (trunk) when there isn't enough room.
ATB,
Phil