Based on this post, it's very unclear if a certificate is needed or not. The most important quote I got out of that post is this:
"I reached out to MS BizTalk support and they asked me not to use the certificate and just use FTP over SSL without certificate. We also changed the ftp firewall mode to passive and allocate storage to no."
Also consulted this post. If FileZilla client can connect and send a file to a customer/vendor without a local certificate, then why would BizTalk need one in an FTP SendPort?
And secondly, if it is not needed, in what circumstances would you use it on an FTP SendPort.
It's my understanding that the certificate is some certificate related to the BizTalk host account's personal store on the BizTalk machine, and not the thumbprint of the customer/vendor we are communicating with.
For BT2013 this is MSDN's mysterious definition:
Specify the SHA1 hash of the client certificate that must be used in the Secure Sockets Layer (SSL) negotiation.
Based on this hash, the client certificate is picked up from the personal store of the user account under which the BizTalk host instance is running.
This statement gives no guidance as to when it is needed or desired. This is the other good blog on the subject, but also implied cert is needed, in contradiction to Microsoft support in early link.
You need to use the client certificate, when the FTPS server requires authentication with the client certificate. And you do not use it, when the server does not require that (what is a way more common).
FileZilla does not support the client certificates at all. If you are able to connect with FileZilla, your FTPS server does not require authentication with the client certificate. So you just leave the respective field in BizTalk blank.