In help from bitcoind -h it specifes that conf can only be used from the commandline. However, if conf is set in a bitcoin.conf file, there is no error and from reading the logs it seems as if the conf=<other file> is being used, despite it being ignored. To recreate, you can setup a bitcoin.conf file in the default directory, add conf=<some other file>.conf and in the separate config file set whichever config value you want and verify that it is being ignored. alternatively, if you set includeconf=<some other file>.conf , your config in <some other file> will be picked up.
This PR fixes this by having the node error when reading the config file if conf= is set.
Additionally, it was mentioned in a recent PR review club that if reindex=1 is set in the config file, the node will reindex on every startup, which is undesirable:
17:14 <larryruane> michaelfolkson: Reindex is requested by the user (node operator) as a configuration option (command line or in the config file, tho you probably would never put it in the file, or else it would reindex on every startup!)
This PR also has a commit to warn if reindex=1 is set in the config file.