Weird transmission

Not good.

Sounds to me like timingchain slop. I never heard that sound before on this engine.
Take a long screwdriver and hold it up to your ear and put the other end on areas of interest. Hold it to the valve cover the timing chain is attached on the left side of the valve cover. That’s the front of the motor. You can isolate sounds with the screwdriver.
Listen through it.

Have you ever run the engine so low on oil it threw check engine lights?

How has the oil maintenance been managed?

 

How many miles?

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Wouldn’t @JC91006 be able to help with this answer?

 

One thing can be an issue is ignition coils..
They can make weird noises.. the engine can be misfiring makes a weird knocking sound.. often goes away at higher RPM..
Or as someone else mentioned could be timing chain tensioner. Can use a stethoscope or a long screw driver put it to your ear and put the point to the part you suspect and listen to the engine.

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It's really hard to accurately hear a sound over the internet, but If I were in your situation I'd look for vacuum leak for an easy solve, failing that a full clean & inspect of all things intake to ICE also Toyota techstream software is well suited to this one....

 

Ignition coils are available at Rock Auto for $20 each. Easy to change. Get new plugs while your at it.. don't go cheap on the plugs. NGK, or Denso.

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Not necessarily, often ignition issues seem to smooth out above a certain rpm.
Coil pack issues are a known problem as they age..
If you had a real trans issue I think you would hear it at all different speeds.
Worth a shot... If you know someone with a Prius that runs well worth no issues you could swap there could.. noise goes away.. you have a confirmation on the diagnosis.

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Listen where the noise comes from with screwdriver or stethoscope. If noise comes from the engine you probably should just replace the engine.

If the noise comes from transmission or flywheel it probably just engine running unevenly. Then you can try to identify the problem with scanner. Fuel trims should tell you if it’s vacuum leak or fuel pressure. Misfire monitors should tell you if it’s a single cylinder. Then you can find out if it’s plug, coil, injector, or something else.

 

Wow you put a lot of miles on this car in such a short time.

When you purchased this car, you asked about the transaxle fluid and I told you everything was New in there, including the seals. So the fluid change you did was a bit early with less than 20k on the fluid.

The car has never run low on oil, the previous priuschat owner was very meticulous in the maintenance of that car. It didn't burn much oil either.

I think you should look at the coil pack and plugs again. Cheapest route to take.

As for the $2000 you've spent on battery and tires, that can easily be resold for 3/4 of your money back if you need to sell it

 

No warning lights would mean no stored codes?

 

I remembered you recently did the plugs and valve cover gasket. I think you should revisit that repair work and make sure the plugs are seated properly and not loose.