Answer to the questions Q2 and Q3 are as follows:
"Q2: For VDDA and VDDD, is it better to offer independent analog and digital supply?"
--> Yes. It is better use separate voltage sources if you have the provision.
--> In general, VDDD can be supplied through Batteries as the voltage of the battery changes over time.
--> The VDDA voltage should be recommended to be stable as the performance of analog components varies a little with change in voltage. However, the components like IDAC will work in wide range of VDDA voltages.
"Q3: For bypass capacitor between VCCD and VSSD, What is the recommended capacitance value? 0.1uF or 1uF?"
--> You can use the datasheet specified value i.e. 0.1uF (page number 14).
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The VDDA in the device is not regulated. Then again there is regulation inside the analog subsystem which helps in the working components like SAR ADC, CTB. There are bias current generating circuits and bandgap references which works irrespective of the exact supply voltage. The component specs guaranteed in the datasheet are met if the supply voltages are within the mentioned limits.
Now additional to what I have said, if you are using SAR ADC with voltage reference as VDDA, the variations in VDDA will affect the result. This can be useful if you are measuring a signal which is also dependent on the VDDA supply. If the input signal is independent of the supply, it is always better to use an independent reference like Internal Vref.