Shouldn't affect sound at all, except, slightly possibly at 800-1000 Hz frequency range during greater than 105 dB of playback.
I wouldn't worry about sound quality.
If I recall it's a 4" port? I could be off. See if others are like this as well, if not, ask for an exchange (you deserve it plus, it might affect your resale value later on!).

You can buy those size covers after-market, but I'm nost sure if they have the pre-drilled screw-holes the Paradigms have.

If I were you and in fact other new PW-2200's have these covers (double check, mine was v.2, not sure what version these are on now), exchange it...accept nothing less...tell your dealer it affects your resale value and possibly performance...he shouldn't care.