You can refer to these KB article below. Please note that SCP is not protocol to use for Winscp and we recommend using SFTP.

https://beyondtrustcorp.service-now.com/csm?id=kb_article_view&sysparm_article=KB0016961

https://beyondtrustcorp.service-now.com/csm?id=kb_article_view&sysparm_article=KB0017001

Although Secure CRT is not stated as one of the supported platform for Password Safe we do have customer using Secure CRT with Password Safe. There are some configurations that need to be done, you can reference the putty registry configuration for Secure CRT.  

I can say that Secure CRT will work fine even with MFA TOTP but Secure FX had issues and I could not get it to work with MFA TOTP, without MFA and TOTP it should work fine. WinSCP will work best with and without MFA TOTP.  CLI based SSH will also work in most cases but you might need t get creative with escaping special characters and only supplying a password to a specific password prompt depending on the solution. MobaXterm will also work but having the SCP/SFTP browser open in parallel with you SSH session will not work. That’s my experience so far.