I seem to have solved this. I referenced the incorrect keystore in step 2 above.
This worked:
keytool -import -alias our_root_cert -keystore “C:\Program Files\KNIME\plugins\org.knime.binary.jre.win32.x86_64_1.8.0.252-b09\jre\lib\security\cacerts” -file our-root-cert.pem
There is also this solution - editing knime.ini to tell Eclipse to use the Windows certficates, although I did not test it myself: