~/.lircrc is the default path squeezelite uses if no filename has been specified with the -i option.

This has been fixed in picoreplayer 5.0 as we now include the path and filename with the -i option.

For 4.1 I'd suggest putting your file at /usr/local/etc/lirc/lircrc as you suggested.

Then add usr/local/etc/lirc/lircrc to the end of /opt/.filetool.lst and save your configuration.

Then your file will be restored whenever you reboot pcp.