Very appreciated for your questions. pls find my comments on your question sequently.
Yes, actually we provided two ways to clamp the differential input common voltage to 2.5V, one way is to use internal Vbias function as you mentioned, another way is to use resistor divider to limit the common voltage in front of circuit, I think both of them are work for TC.
D1,D2 intend to protect Iout1,Iout2 pin during over voltage input, but if considering D34,D35 in series of Iout1 and Iout2, strictly speaking we can remove D1,D2 with low risk for normal function, but still proposed if considering in noisy environment.
Actually you may found we leave two option for 5V selection on board, both ADP1720 and ADuM3471's interal 5V regulator, you can switch them by jumpers. While ADP1720 can bring more clean and stable(low ripple) compare to ADuM3471's internal 5V. And also, ADuM3471's internal 5V can only output limited current compare to ADP1720.