In 2.0.1 and 2.1, if you have interfaces setup with a manual address, then pfsense will create a manual rule for them when switching from auto, the first time you do it. From then on you have to create your own rules.
If you are running clustered firewalls, then you most definitely want it using the CARP addresses. Nothing should be using the physical address except for the localhost (127.0.0.1).