First time I've heard of the fungus amongus theory, I live in the desert so apart from a rainstorm every 3 months or so the boat stays really dry.
I'd be pretty certain it was the dye from the black cover on the vinyl. I'm no expert but I don't think fungus could grow over the whole rear engine cover in the hour or so between the rainstorm starting and me checking it. It did dissappear with an assortment of vinyl cleaners and some time in the sun.
For the grey cover, I got some similar discoloration on the rub rail where the cover touched but nowhere near as dark. I think it had more to do with the treatment on the back of the cover than the cover itself. Rubrails are pretty dense plastic, not much for fungus to cling onto. The only thing I found that really got it off the rubrail was wet/dry sandpaper. I've tried soft scrub, bleach, acetone, comet and pretty much everything else in my arsenal to clean the rail but I'll give some tough-actin' Tinactin a try if you think it would help.