Yes, dogs can change colour as their coats 'blow' (hairs get old & start to shed, often lighter in shade,eg gingerish on a brown dog, but the new coat would be usually darker & shinier. Coats vary in how liable they are to sun-bleaching, & depends on sun intensity, & perhaps pre-disposing factors like being in water a lot. Coat colour can be affected by foods with pigment in them, eg sugar beet, food dyes & seaweed can darken light fur. (my palomino horse was ruined for a season's showing by winter sugarbeet feed, (coat went reddish) & another Spring after adlib seaweed powder, his hind quarters grew dark brown fur, which gradually disappeared by end of June thank goodness!- I think dissolved out by rain, as not groomed a lot. (He's normally bright gold in summer, pale gold in winter) Sugarbeet is often in dog foods (perhaps more as a 'filler or fibre in cheap foods?), & a rescue place might likely be using cheaper foods, which may also (I guess!) have food dye added by manufacturers to make the feed look better to human carers (like some dog treats seem to be). The effect of this would wear off in time, according to when it was last fed the color factor. If you knew the exact history of the dog it may shed light on the feed situation-eg.if it was starving somewhere, it may have scavenged dark coloured food-sources
Some species can change colour temporarily for camouflage, & maybe under stress in rescue situations there may be a trigger in some dogs to darken the colour, as that may lower its risk profile, as it might in wild species??
Shelter / rescue people are often wrong (in my long experience as trainer/ rescue /dog breed info/ behaviour work ) in guessing breed mixes, & tend to stick to info given by the previous owner, & even first-time owners are given incorrect info, (pups in one litter can have more than one father & not be pedigree as supposed) so the dog may be carrying colour genes/alleles which are not expected. Google dog color genetics for lots of info.Dogs with sable genes change colour & pattern dramatically while growing up. Merles tend to grow more & more dark hairs, & roan spotting increases with age too.
Good breeders /websites to do with Chesapeakes & Pyreneans may be able to advise on likelihood of colour change through age/feed etc. (google 'Chesapeake retriever coat color' etc).
Hope some of this is helpful. Glad he's got a loving home now!