This is current/amd64 on a PC. It seems that if MANPATH is set (to something nonempty), the settings in /etc/man.conf get ignored:
$ cat /etc/man.conf
output paper a4
$ man -Tps true | grep PageSize
%%BeginFeature: *PageSize Letter
<</PageSize [612 790]>>setpagedevice
$ env | grep MAN
MANPATH=/home/hans/man:/usr/local/man:/usr/share/man:/usr/X11R6/man
$ export MANPATH=
$ man -Tps true | grep Size
%%BeginFeature: *PageSize A4
<</PageSize [595 841]>>setpagedevice
Jan

