The knocking noise experienced by OP is very similar, if not identical, to that noise in my 2017 2nd gen 3.5. The remedy by my dealer was replacement of both VCT "phasers" (because they could not clearly differentiate noise from the intake vrs exhaust VCT actuator) on the passenger side valve train. This fix absolutely fixed the noise and still quiet 3000 miles later. I don't believe this noise shown by the OP is anything related to the HPFP, which makes a subtle "thumping" noise clearly different than from a defective VCT actuator. As a test, the use of a simple inexpensive mechanics stethoscope can show location and type of noise difference.
My engine noise was apparent only at hot idle, and not during cold start up nor warm up; it showed up maybe 10 minutes into hot idle and thereafter. My research has now shown this issue may be a common noise issue with many 2nd gen 3.5's very often diagnosed as a HPFP issue or with no action by the dealership because there are no visible codes, no performance issues, and no Ford TSB or SSM issued to date. I am surprised that Ford has not issued a TSB to date. Keep in mind my correction required 3 trips to the Ford service dealership, with the last visit clearly communicating what I gathered from the Ford forum sites and with confirmation of noise and location by their experienced tech who also felt the noise/vibration while touching the area above the phasers near the two VCT solenoid towers and strongly suspected one of the phasers. See attached picture showing location of the phasers, which I understand were redesigned and smaller than the 1st gen 3.5. I suspect there may have been a bad batch of phasers by Borg Warner with quality issues, but could not be sure. Other forum people have concern for oil passage issues and flow to the VCT's which can cause noise issues.
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