The Vref value is determined when you build the firmware.
CapSense component refers the VDDA value which is set by System tap in .cydwr in PSoC Creator project file.
So, CapSense does not follow the measured VDDA in run-time, but fixes the Vref value with your input.
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If VDDA is +3.3V but System tap's VDDA is set to +1.8V, real vref is 1.2V.
If VDDA is +1.8V but System tap's VDDA is set to +3.3V, the calculated vref=2V, real vref is can only reach 1.5V~1.6V, but this setting way is wrong, please don't do that at any time.