Overset better than underset?
The neck is a little overset, but as long as this is not excessive it can be a good thing as the the neck/body geometry changes over time. Your string height above the body is quite low, but that’s only really an issue if the sound is found wanting.
When setting a neck I aim for around 4 mm of saddle protection above the bridge, but tiny adjustments in neck angle can make a significant difference at the bridge.
You certainly need a better fitting saddle though. Even with an under-saddle pickup there shouldn’t be an obvious gap, the saddle just needs to sit in the slot without undue pressure. The same goes guitars without under-saddle pickups to my mind, if the saddle is tight in the slot any bridge shrinkage can cause cracks.
Your current setup figures are near perfect, so I’d get a new bone saddle made that fits properly and copy the top surface shape if intonation is already spot on. My bet is that in a few years you may be glad of the extra saddle height.
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