If you are willing to give up on any Sonos consideration you could open it up and see what you could do.

The warranty is pretty clear at one year, anything after that is just Sonos being nice.

Extended warranties are available and if you need / want more than the Sonos standard term you need to purchase one.

Do you have pets, small children, or ‘critters’ that may have deposited something inside?

I have kids, but no - nothing inside. 

I have picked it up and given it a good shake, no rattle sound could be heard. 

it’s strange that only during low frequency, it starts to rattle/vibrate - almost like it’s overpowered, 

also, when I lie it flat on its side, the rattle , vibration seems to be a lot less.. 

You’ve probably already done this, but make sure that it’s not something nearby that is rattling. When I first started using SUB I found a lot of windows that needed attention because they rattled. Sometimes you’ll find items inside walls that can rattle at certain frequencies.

If you are sure that something inside the SUB is making noise, you can probably find disassembly videos and poke around inside. The noise maker should be obvious after a close visual inspection. Be careful what you touch because there are high voltages inside the unit that may not discharge immediately after power is removed.

 I had a rattle that was apparent at a certain frequency using a Sub Gen 3.  It was not easy to track down.  Finally I found out the side panels of my TV rack were rattling.  A couple of door stop wedges crammed between the middle shelf an the side panels took care of that.

I’ve taken the same sub to a more spacious living room, connected it to the beam to test. 
 

same scene in the same movie trailer and I still get that rattle , vibration 

the way I’m testing it is I have my ear right to the sub cavity - quite apparent the vibration and rattle is coming from inside .. 

Might be as simple as a loose cable or connector and easy to fix. Doing so negates the Sonos replacement offer though, I’d risk that in your situation.

If you can pick it up and try a good shaking to see if you can get whatever is rattling to move somewhere it won’t rattle.

Look for a good tear-down video so you can get in and out with minimal damage.

If you find something take a picture and post it here to help other folks in the same situation.