I doubt that the geothermal system will affect the foundation noticeably unless the soil is highly expansive. If so, raising the temperature of the soil could result in shrinkage and settlement.
If the building is wide compared to the depth of the boreholes, or if a horizontal system is planned, the presence of the building may tend to trap the transferred heat below the building. Such a system depends on the ability of the ground to radiate and/or exchange heat with the air to remain near the average annual temperature. Putting it under the building may cause the temperature of the surrounding ground to rise or fall (depending on whether your heating season or cooling season is the greatest demand)and reduce the efficiency of the system.
Better consult an expert.