My first thought was along the same lines as Colin but, as he suggests, it will all end up quite a bit darker and the difference may still be visible.
If it was myself I would ask the vendor to exchange the kit and, if they refuse you could try approaching Aeronaut themselves for a replacement. At the end of the day I would not consider that sheet to be fit for purpose. The trouble is, if you try to do anything yourself first, then you will never be able to exchange it and you will be stuck with it.
The first thing would be to contact the vendor and tell them you are not happy with it. If they start trying it on with wood being a natural product and there is no guarantee of colour etc..etc.. then point out that variations in colour does not include a completely different colour between some components, the two sides of the cabin being two totally different colours and the transom being half one colour and half another colour. The colour variations you have in that sheet are, to me anyway, beyond reasonable.