The availability of SCP is irrelevant. What matters is support. I'm glad you did your research but you came to the wrong conclusion; the conclusion you should have come to is that FTP is much more tightly integrated. In C# it's part of the standard library; in Java it's an Apache library everyone has.
I think you're overvaluing what is the "best" method of file transfer. When you have to set up a file transfer process with a client, and tens or hundreds of thousands of dollars are on the line, you are going to choose the path of least resistance. That path is FTP. Clearly. If you are the much bigger company you have a better chance of doing things the "right way" but that rarely happens just because these are ultimately business decisions and business doesn't care about implementation details unless they cost money.
I think you're overvaluing what is the "best" method of file transfer. When you have to set up a file transfer process with a client, and tens or hundreds of thousands of dollars are on the line, you are going to choose the path of least resistance. That path is FTP. Clearly. If you are the much bigger company you have a better chance of doing things the "right way" but that rarely happens just because these are ultimately business decisions and business doesn't care about implementation details unless they cost money.