Black rectangular plate on transmission

Pictures always help, but my WAG would be the opening for a starter.

Does it look like it would align with the flywheel?

 

Perhaps the parking pawl motor assembly, but that's kind of round. Definitely a photo opportunity.

Take a look at the photos in this link. Can they help you ID the plate?

04 05 06 07 08 09 Toyota Prius Automatic Transmission Assembly CVT OEM 157K | eBay

 

Here is a picture of a Gen 2 Prius Engine/Transaxle, can you point out what you mean?

From 1:25:35 to about 1:30:35 he shows electrical connections below the rectangle above with the Orange wires near it. (This is a Gen 1, but Gen 2 is similar)

 

Little access hole into the bell housing. If you pop it out, you'll just be looking at the flywheel.

Sort of traditional, I remember similar holes on cars I had years and years ago. If the transmission was an auto, you might need to work through it to reach the torque converter bolts. Not much use for it with a manual.

Also not much use with a Prius, but reportedly if you've been having misfire rattles for long enough, you can reach in there and down and see if you can scoop out any pieces of the damper springs.

 

Really you won't see anything through there but the back of the flywheel. It doesn't growl, unless you move suddenly and it doesn't know you.

 

Sometimes posting a recording is helpful. (Especially if you listen to it yourself first, or have a friend listen, make sure it is audible and make sure somebody else can tell what sound in it is the sound you mean. You'd be surprised how many people post recordings without checking that.)

You'd be surprised how often really horrible growling noises can turn out to be really simple things, especially if they come and go like that, things like loose heat shields or exhaust bits that make contact with the body.

But a recording ....