My pre-159 wheels (SAAB 9-3 Convertible) had identical markings on the roof. The car was also an ex demo and had probably been sitting in the showroom roof down for some time, but to be fair the marks didn't really appear (and then very gradually) until maybe 9 - 12 months old.
I always followed 'good practice' with the roof...never putting it down damp or wet, never leaving it down for long periods (eg overnight), cleaning with soft brush every wash in the direction of the fabric grain (occassionally using persil liquid or renovo cleaner) and about every 6 months giving it a coat of renovo ultra proofer (great stuff - used to make the marks less visible and great water beading). The car always lived out doors all weathers too.
So overall the roof was in excellent condition when i sold the car (4.5 yrs old), no algae, marks, nice even colour, but nothing got rid of the lighter marks! I also think the ones that run across the roof are caused by gradual wear of the fabric on the runners as the body flexes when you drive. The angular mark is also the fold crease, and I guess also experiences rubbing and movement when the roof is stored and the vehicle driven.
Just before the end of the warranty I pressed SAAB for a new roof - refused! dealer said they all went like that...and sure enough all of their stock showed similar marks, many worse than mine on 1 year old cars. My roof was blue, and the marks seemed worse on black roof cars.
If I'd kept the car, I would have soon gone down the dye route (again renovo do one for DIY) but baby arrival prompted thoughts of more practical transport! I was never sure though that the marks would fully go with dye, perhaps just tone in better.
In summary, i think what you've got is normal 'wear and tear' (maybe not being helped by the roof being stored down by the dealer, but i don't reckon there's going to be a lot you can do about that now). There's lots you can do to keep a soft top roof in good condition, but it is the part of the car which will wear visibly and can't be completely avoided.
I too am a car care perfectionist so I feel your pain! But I came to terms with it...afterall a soft top should have the roof down at all possible opportunities anyway, and you can't see the marks then!