Keep in mind that in your two way system with a 5" "woofer", that "woofer" is designed to produce all the midrange band and and a little bass as well. I cannot see a crossover point listed for your speaker. to be honest, that speaker doesn't really produce bass, but upper bass at best and it tends to have a boost in that area in order to give the illusion of real bass. That may be your real complaint.
The cabinet volume and ports affect the deepest lows it can reproduce only and anything above that should not be affected but, then again, your woofer is actually a midrange driver that produces a little bass to go with it.
As for the sock, it does change the overall sound of the woofer, and perhaps the midrange as well, thereby affecting the entire balance of the system as a whole. If the woofer produced more midrange than you think, that may be affected as well.
Many tweeters and separate midranges are sealed back designs so the cabinet volume would have no affect on them.
As for any thermal damage, don't worry about it. If you overdrive it, you'll hear sounds of strain long before anything happens.
No offense intended, but the sock idea works best when dealing with somewhat larger systems where real bass is part of the equation. I honestly think it's the inherent nature of your speaker that bugs you.