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Hello,
Yes, it is definitely possible that the capacitance value measured with the FDC1004 will be different than the capacitance value measured with an LCR meter. The FDC1004 is meant to detect changes in capacitance, not replace an LCR meter.
If the liquid is conductive, it is possible that the liquid will drain charge from the electrodes. For this reason, the FDC1004 is not suitable for measuring the level on conductive liquids. For water this is not a concern.
Unfortunately the detailed operation of the switched capacitor circuit is proprietary and I'm not able to share it. The only additional information I can offer is in this blog post.
Best Regards,