How I see it, may not be accurate since I don't use Squid since a long time:
When you are using Squid, the connection is no longer between the host and the web server.
The connection is between pfsense itself and the webserver, thus the definition of proxy.
The rule in which you applied the limiter will no longer be used.
Transparent or explicit proxy, both are affected by this behavior.
What you can do is to enable limiter in the squid itself, or set limits through Radius if you configure squid to authenticate through it.
I didn't test the Radius authentication with Squid, so I'm not sure if it would work.