I remember from an ACI special publication on mats that for piled mats the measured midterm of the installed system at the Messeturm (a 300 m tall building) and another important building approached a 50% sharing of loads between piles and mats, i.e., the piles would be taking themselves only half of the column loads.
However, I will repeat: except for VERY stiff foundations or foundation plus buildings, the magnitude of the settlement dependes mainly on the magnitude and position of the column loads, i.e., for most cases, I would say, except where it is worth to prove otherwise, it may be useful to think of the foundation be flexible for settlement account. However, that -properly- can't be said without a soil-structure interaction analysis, and likely that's what the geotechnical evaluation can be giving if it has not been counting with the stiffness of the foundation plus building above. So you may first investigate what difference would make in settlements the loads be applied directly on the soil without consideration of the foundation (more or less equating to the geotechnical assumption) and when made with your actual building imparting the loads to the soil. If there is significant difference the estimate of the gotechnical report needs be corrected to account for the standing stiffness of the building. For most cases it won't make a difference but since a piled mat yours might still be one of the cases where foundation plus building stiffness has a say.
You may make a simplified first try by putting in a notional mat the added stiffness of all floors and then support it on stiffer springs at pile points and weaker springs elsewhere, then apply column loads to that piled mat. If, after proper tuning of the springs, your settlements differ in more than say 20 or 30% from those given by the geotechnical report for a significant protion of the area, i.e., you have settlements about 80% or less of those given by the geotech estimate, you may use your standing stiffness and then use your (or other better estimated values) settlement values to account for distortion or deflection issues. For most other cases it may be simpler to add directly an imposed settlement as specified by the geotechnical report at column points, and combine with every service level to see the effects on deflection control.
This same component settlement hypothesis equally without any factor, i.e., with factor 1, should be added to any of the structural strength hypothesis checks.