Retirement tax questions

"If you are an S-corp and have an  EIN, the company you worked for would not send a 1099."

It is their sole discretion. I was told: we don't do corp 2 corp. Only 1099 or W-2 with individuals. And for you it will be 1099.
I have no idea what their reasons are but this is what I was told outright. 

To be fair, I didn't have an S-corp or LLC formed yet when I signed the contract but I asked them if they would consider signing with an S-corp of my friend. And they said "no". 
So all this talk about what I should have asked them to do/ should have told them is  pointless. I am where I am

Thanks a lot for your help!