If they packed all around the ducts it may be a part of the frame that's doing it. What about the HVAC where it comes through the wall. Is it in that area?

 

I try to put my ear near the sound source, it sound loudest if I listen close to the gear stick.

 

These dealer techs can be rather poor. This sounds like it's a drivetrain issue.

 

Could it be a heat shield that is vibrating?
That could echo thru the dash??

 

Blah, Blah, Blah

 

Don't go chasing after heat shields. They are not susceptible to temperature changes like that since they are always hot.

 

Heat shields and exhaust components do become loose and vibrate.
Especially with the engine vibrating
Which then tells me to check your motor mounts.
All this is of course guessing since I can not be there to see what is wrong
And have no way to test anything to lead to the cause of this issue.

 

I have three issues with my Civic:

1. The rattle sound comes from (where the gear stick is, best I can tell)
2. On backing up the car from the garage with a light foot on the break, I hear a screeching sound from the break
3. Car vibration

For # 1 & 2, issues only happen during the early morning or late night. I have not been able to show it to the dealer lately. What options do I have? Want to get repairs done before the warranty runs out.

See the video:
Issue # 1 usually come with this rattle without the vibration (see video above)
Issue # 3 is almost always without sound (see the video above)

The car has 20k miles on it!

For issue # 3, the dealer says it is normal for Civic, is this correct?

 

I had a similar sound. Thought it was coming from the engine bay.
When I went underneath the vehicle, I saw a broken exhaust pipe which was rattling.
Based on what happened to me, may have nothing to do with your issue, I would say to look under the car
Check the exhaust for loose pipes or heat shields. Better done when cold.

Brake squeal? Would need to look at the brakes and check the pads.
Could be worn?

 

Does break pad go bad with only 20k miles?