They are wrong. The fuse is to protect the cable not the fan.
Neither an isolator nor local fuse is required by the regs if it is on the lighting circuit.
Is it though? I'd need to check the blue book as I always treated it like a shower isolator where DP isolation is required.
My understanding of manufacturers instructions are that they should always be followed and that the mention of a 3A fuse is to reduce the likelihood of the fan catching fire if it seizes.
This may be the fan manufacturer covering their liability, but if I ignore the instructions then I become liable.