A quick google shows some did indeed have yellow bonnets.
That second picture is a "restoration" that someone's had a go at by picking up pictures of CG 90's or Defenders. We didn't get the small side battenburgs until the 1990's (our D-reg 90 didn't look much different from the S2a's / S3 paint jobs), the light bar is a premier hazard one and it should have been a single beacon on a S3, and there are a couple of other bits that aren't right.
scottuh ref the yellow bonnet, although we didn't get a yellow bonnet on our vehicle until our 1996 Defender, it could depend on how long the vehicle remained in service for. Even if it was originally delivered with a blue one, Coastguard Landies tended to remain in service for a long time, as they generally cover quite low mileage, so it could well have been either repainted or even completely replaced as manxcat stated above. The bonnet would have been a great flat surface for dropping things on when using the front winch on cliff operations, so I wouldn't have been surprised if it's been dinged and bashed over its time in service. It almost certainly would have been delivered with a bonnet mounted spare, I don't know of any of the CG Series vehicles that didn't have one.
The number plate could have come from any part of the UK as you've discovered. We used to buy in vehicles in bulk and they got allocated all over the place, often a vehicle from one place would be re-allocated to another station if it was deemed to be necessary. For example, our old Defender got moved on to another station when we got allocated an L200, as it was still newer than their vehicle but their station was too small to garage anything bigger than a Landy.
Nowadays the vehicles are all sourced from a lease company and sent back there when released from service. For a short time we even got to pick the letters - you will find a lot of (ex) Coastguard Defenders running around with *CG suffixes.
Unfortunately gone are the days of CG Landy's. they deemed them unsuitable a few years ago due to lack of airbags etc and as far as I know there are now less than a handfull in the organisation.