There was an issue with loading config files for in-process runs in 3.16.x of the console runner (nunit/nunit-console#1390). Some investigation found that a past feature to specify the config file on the command line was added as far back as v3.8 of the console runner but never documented (outside of the release notes)
It was added in PR nunit/nunit-console#348 to resolve issue nunit/nunit-console#246
It expects to be passed in the format --configfile=custom.app.config
I'm unsure where all it may be helpful to document. The existing pages I looked at for this info but didn't find it were: