Installing Mac os x 10.11 El Capitan on clean hard drive using Windows
Solution 1:
The Mac Pro 3,1 is a difficult Mac to boot without a system disk in. Many people claim they will boot from USB - 13 years of contradictory evidence is on my side ;)
I'd say you need a ready-made bootable system disk, & Windows is not going to provide one of those, I'm afraid.
If you have a friend with a Mac that will still run El Capitan, take your drive round to them.
Alternatively, if the SuperDrive is still working - those don't necessarily last 13 years either - then buying a Snow Leopard* install CD/DVD on eBay could be your get out of jail free card.
As a final, if bulky, alternative, any Apple Store will do it for you. I don't know if the Apple Store would install to just a hard drive/SSD if you handed them one - but it might be worth asking.
*Retail version, picture of a cat on the disk, not grey ones which can be Mac-specific.