"I rarely get the case of the camera focussing too close."
You did in your fist picture though Ian, but in the second one that nearest spine is now out of focus, however you were probably restricted by what depth of field you have available as to what you could get in focus. Generally speaking the eye notices out of focus objects nearer to it more than those behind the point focused on.
The problem with close up's using autofocus is the ideal focus point may be between two objects where there is nothing for autofocus to focus on. Using screen focusing you can often spread depth of field over the two, whereas autofocus would either focus on the front one putting the far one out of focus or vice versa.
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What does amuse me though is sites that recommend switching off autofocus for macro photography then say use the focus confirmation light in the viewfinder to confirm focus in manual. The focus confirmation light works off the autofocus sensor so it will be no more accurate than leaving autofocus switched on, so ignore it. Using your eye looking around the focusing screen to determine what is in or out of focus in manual mode when close up is the only reliable way.