If you'll be using CP then you shouldn't run transparent Squid on that same pfsense system.
I guess it's a matter of personal preference, but I'd prefer to run disk-intensive software like Squid on a separate system anyway, with its defaults tuned to be a "server". Others prefer to have an all-in-one system, running a dozen services (e.g. antivirus, caching proxy, URL filtering, reverse proxies etc).
IMHO a reasonable compromise would be to run a couple of VMs on the same physical server.