The new location of the PID file needs to be added in the bundled apparmor profile. Without it starting the service will fail with something like this:
--AVC apparmor="DENIED" operation="mknod" profile="/usr/sbin/squid" name="/run/squid/squid.pid" pid=64342 comm="squid" requested_mask="c" denied_mask="c" fsuid=0 ouid=0
... FATAL: failed to open /run/squid/squid.pid: (13) Permission denied -- Trivial patch attached.
--- /etc/apparmor.d/usr.sbin.squid.old 2020-05-04 09:57:54.000000000 -0700 +++ /etc/apparmor.d/usr.sbin.squid 2020-05-05 23:44:22.227744533 -0700 @@ -37,7 +37,7 @@ # squid configuration /etc/squid/** r, - /{,var/}run/squid.pid rwk, + /{,var/}run/{,squid/}squid.pid rwk, /var/spool/squid{,3}/ r, /var/spool/squid{,3}/** rwk, /usr/lib/squid{,3}/* rmix,