I guess it depends on how he/she did their calculations. Their numbers do seem pretty conservative. How many safety factors were used? I don't know; but these types of analyses aren't like LRFD. It's more likely the "conservative" settlement calculations resulted - in part - from the selection of conservative design parameters...
Think of a plot of skin friction vs deflection as a bilinear curve; at the origin there is no movement - and no mobilized skin friction. At a deflection of about 0.2 to 0.25 inch, the skin friction is fully mobilized. For deflections greater than 0.2 to 0.25 inch, the skin friction remains constant, or decreases slightly (5% to 10%.)
I guess a part of the "settlement" calculation could be due to an estimate of the shortening of the timber pile due to the loading. But that seems to be a stretch -
Are you reasonably close (physically) to the geotech? If so, try to arrange a face-to-face meeting. Ask him/her to give you a detailed explanation of the settlement estimate. Why? Because it is driving the structural design toward a significantly more expensive solution, and you need to understand what's going on so that you can explain it to the owner. I've had a few of those meetings. They can be uncomfortable; but a good design professional doesn't mind explaining "why" at a technical level.
If he isn't close, call and tell him that you need for him to "talk shop" with one of the geotechs in your immediate area. Be sure to hire your local geotech directly; this may be important in the future. If your local geotech thinks the geotechnical engineer of record (GER) is blowing smoke, you'll need to go to the owner and ask for another study. But the odds are that the two geotechs can hash things out, and the GER has a reasonable basis for what he/she is recommending.
Regardless of the answer, you need to have enough confidence to go to the owner with some sort of recommendation. I don't think you're there yet.
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