Manulife is asking me to apply for CPPD. As part of the agreement, I’m being asked if I want any retroactive benefit to go directly to Manulife from CPP. Are there any pitfalls to this that I should be aware of?

This is quite common when dealing with insurers, and typically they are entitled to that retroactive benefit, as well as a credit for any monthly benefit going forward. You'll want to ensure that you keep your insurer informed of any income you receive from CPPD ASAP to avoid any repayment issues down the road.
This process is fairly straightforward, but we created a guide that may address additional questions or concerns: https://stlawyers.ca/law-essentials/canada-pension-plan-disability.
If you would like to discuss further, or want assistance with your CPP application, please contact our disability specialist, Rebecca, at rebecca.stap@stlawyers.ca