Topper dinghies...

I tried a heatgun on a red hull but the result was patchy and inconsistant so I gave up.
The marks on the gunwale near the transom look like collision bruising. The fordeck marks could just be fading patches.
If it holds air I wouldn't worry.
Why do the red ones fade in a circular patch on the fordeck?

They are pressure marks. The one that would worry me is the one at the corner of the mast gate where I suspect a screw has been over tightened.  I would want to know that this hasn't caused a crack that then leaks into the hull.  As for the ones on the gunnel, look underneath and see if there is a crack there or if the deck and hull have separated at all.  Those again can be points where the boat can leak.  The discolouration on the foredeck is the least of your worries, provided there is no cracking.  Colour can be restored through judicious use of a heat gun.  

Or scuffs from the cover that have become a bit more uv sensitive? Could have had some wet kit left under the cover perhaps.

Looks to me like there have been impacts there at some time. No real idea if they matter or not - worth pushing on the bit on the foredeck perhaps and seeing if it's soft or deformed? Not much you can do really whatever it is!