Lextacy01

Forgive me for possibly bringing up something that may have been answered in the past, but time and information could have changed.

I have a 2001 ES300 with a few weird things I have questions about.
My car has this box that is near the sub in the trunk. I have attached pictures. This box now recently has begun to rattle, and my question is do I need this box? What is it, and how can i silence it? I mistakenly took my car to have the sub replaced and noticed that it still has the same issue. I have narrowed it down to this box.

I also wanted to know if factory options that were left off of the vehicle can be added such as: Heated seats, auto leveling headlights, and anything else that may be of interest.

This model was the one to include vvt-i which I know means (from what i have been able to gather from reading this forum) that I cannot* supercharge or increase the horsepower due to the ecu throwing out CEL codes and etc... Does that mean that in the future or God forbid the engine needs to be replaced, that I can put a 98 model engine into the car with a few other misc parts and then supercharge, and or beef the hp up?

This car has the glass only doors with no frame, much like a convertible door (my description at first glance when the window is down with the door open.) What can I do about a dry or now noisy rubber seal? Should I replace this gasket the window sits on, or oil it up?

I have also had very noisy brakes. I took the car to lexus and they said it was because they were non-factory parts used when the pads were changed. They de-glazed the brakes and told me if they squeak again it would likely need to have new a brake system entirely installed. Is this true? If so what options would I have? I would rather spend a few extra dollars to get something far superior, as I think the brakes are rather lacking as they are if they are indeed efficient as the dealership said they are, despite the squealing and odd sounds they make.

Again, I apologize if these questions have been answered entirely before. But things do change over time and I know the experts to ask are all here from what I can tell. And thank you for both reading and or answering this !!