Options given both on cmd-line and in the config with different values

Hello hackers,

I'm trying to understand what is happening in the following bug report:
https://bugzilla.redhat.com/show_bug.cgi?id=1935301

The upgrade process makes it a bit more difficult, but it seems to boil 
down to this problem -- even when pg_ctl gets clear guidance where to 
find datadir using -D option on the command-line, it forgets this 
guidance once finding data_directory option in the postgresql.conf.

Is this the expected behavior actually? Or is the behavior in this case 
(i.e. when the same option is specified on the cmd-line and also in the 
datadir, with different values) defined at all?

(couldn't find it in the doc and even google does not return me anything 
useful)

Thanks for any tips,
Honza