You actually posed two questions.
First was...
abc1234 wrote:
...In Lightroom, the plugin Show Focus Points seems to indicate all the focus points were off.....
CHG_CANON answered this. While your Lightroom plug-in didn't show any AF point, the Sony viewer does show one that was active.
CHG_CANON wrote:
Sony Viewer shows the green box on the gravestone on image-right as the AF location.
And that's precisely what appeared to be the point of focus in the image in the original post.
It appears there's an issue with the Shot Focus Point Lightroom plug-in. I've used that with some other camera systems and did not find it entirely reliable. It sometimes is unable to show the active point(s). I have no idea way. Sony Viewer shows what AF point was active and used in this image.
Other than that I don't see a problem.... Unless the original poster was wanting more of the scene to be in sharp focus, in which case they should have used a smaller lens aperture. (Focus stacking probably wasn't a possibility, since there's so much in the scene that might move from shot to shot.)
As to the second question whether the AF was auto or manual...
abc1234 wrote:
This is what fooled me in the metapicz report:
FocusMode AF-S
AFAreaModeSetting Flexible Spot
FlexibleSpotPosition 440 218
AFPointSelected n/a
AFPointsUsed (none)
AFTracking Off
I read this to mean that though the AF-S mode was selected, it still was not used.
As I read the above...
Autofocus was enabled and set to AF-S ("single shot" AF)... and it was, in fact, used (as proven by the Sony Viewer report that CHG_CANON uploaded).
Flexible spot was the focus pattern mode selected (I'm not familiar enough with Sony to say what this means or what the alternative focus patterns might be).
No AF point was selected by the user, so the camera simply chose a point itself, focusing upon the one tombstone near the tree.
I have no idea why it says "AF Points used: None". Obviously the camera and lens did, in fact, autofocus by using one (or a group) of the AF point(s).
I suspect the last line of info probably will always show "Off" when AF-S mode is being used... That mode should acquire focus, then stop and "lock". AF tracking should only occur in AF-C or "continuous autofocus" mode. The purpose of this line of info is probably to let you know if you enabled or turned tracking off or used focus lock or in some other way prevented AF tracking... while the camera was in AF-C mode. It's not applicable to AF-S mode, is it?