I just purchased a new card from Amazon (EVGA GeForce RTX 3090 Ti FTW3 Ultra Gaming, 24G-P5-4985-KR, 24GB GDDR6X, iCX3, ARGB LED, Backplate, Free eLeash https://a.co/d/38WLZkP)

Does this come with the 16pin to 3 xPCIe connector?

Do I use the 3 of the PCIe 4x750mm that come with the EVGA Supernova 1000 T2 to connect to the 3 x PCIe to 16 pin Connector above

Does the 3 x PCIe cables above connect to VGA1, VGA2 and VGA3 ports on my EVGA Supernova 1000 T2 PSU?

Are there EVGA or 3rd party 16 pin to 3 x PCIe cables that are long enough to connect directly to the PSU? Trying to avoid having two cables. What would these cables be called?

Is the 16 pin to 3 x PCIe cable called a 12PerFE Cable or are these two different cables? It looks like the 16 pin cables requires 3 PCIe cables while the 12PerFE cables only uses 2 EVGA 8 pin cables?

I can only confirm for the 3090 Ti Kingpin, but it did come with the adapters to convert a triple 8-pin into 16-pin's.  Yes, you just plug the normal 8-pin's into the adapter so if you already have three 8-pin's running your current card you can just plug them into the adapter.  You'll see 12-pin and 16-pin used interchangeably in a few places, I believe this is because unless you're running a gen 5 PSU that uses the four pins that communicate between the GPU and the PSU they really only use the six ground and six power pins on the cable. 
 
As far as the FE I would guess that their adapters are dual 8-pin to a 16-pin for cost purposes and based on the real world power draw.  An 8-pin cable's official spec is 150w per cable, but they've been able to produce well past that for a long time and any power supply capable of running a computer with a 3090 Ti will allow far more wattage.  You see this with the XOC runs where a triple 8 is pushing upwards of 1000w on LN2.  Between the 75w from the PCIe slow and the 2x 8-pin there is more than enough for the official 450w the card draws.  The AIB's tend to allow extra power and need to over do a lot of things to stand out, which is likely why you see the triple 8 adapters.

USMC7312
I just purchased a new card from Amazon (EVGA GeForce RTX 3090 Ti FTW3 Ultra Gaming, 24G-P5-4985-KR, 24GB GDDR6X, iCX3, ARGB LED, Backplate, Free eLeash https://a.co/d/38WLZkP)

Does this come with the 16pin to 3 xPCIe connector?

Do I use the 3 of the PCIe 4x750mm that come with the EVGA Supernova 1000 T2 to connect to the 3 x PCIe to 16 pin Connector above

Does the 3 x PCIe cables above connect to VGA1, VGA2 and VGA3 ports on my EVGA Supernova 1000 T2 PSU?

Are there EVGA or 3rd party 16 pin to 3 x PCIe cables that are long enough to connect directly to the PSU? Trying to avoid having two cables. What would these cables be called?

Is the 16 pin to 3 x PCIe cable called a 12PerFE Cable or are these two different cables? It looks like the 16 pin cables requires 3 PCIe cables while the 12PerFE cables only uses 2 EVGA 8 pin cables?

The 16 to 3x8 pin adapter comes with all the 3090Ti models EVGA have, they are within the package, so unless you buy used or from an unauthorized reseller where the package might have been opened, you will get it.
The Amazon purchased card will not be any different.
As for your 1000 T2 and the connectors, you can have the three 8 pin connectors connected to any three available VGA/PCIe connector, for cleanliness sake or for you to be able to zip tie or velcro the 3 cables together (to manage them better), you can connect them next to eachother for example if you like.