I imagine the reason PMDG say what they do is that the real 777 has a flybywire system which is similar to the Airbus philosophy of the computer intercepting the pilots inputs, and producing an output to the control surfaces which the computer thinks is best. The PMDG 777 will try to replicate this, and needs normal FSX inputs for it to work, otherwise you will probably lose things such as bank angle/stall protection, and not get the control surfaces to move correctly. Should only apply to aileron and elevator controls.
The Airsimmer A320 (FS9) has the same requirements. The PMDG MD-11 is the same for the LSAS system, although in that I find I can assign in FSUIPC as long as select "send direct to FS9".