Sorry, I'm not sure if I understand the idea. You want to store the master password into a file protected by another master password? Where do you get the latter one from?
My explanation was confusing, it was late...
When you enable the master password the very first time, and you request the master password to be stored in the parameter file then WinSCP would use an internal key to allow decryption/decryption of the parameter file. That key would not be typed in plain text but would be known only to WINscp and possibly contained within the binary. Heavily obscured and unique to each Winscp installation.
WsFTP does something similar, all the passwords are encrypted but you do not supply a plain text master password as WsFTP has its own master key. WsFTP isn't open source and I think the key can be stored in the binary. I do not know whether the WsFTP key is unique to the installation, I suspect it isn't.
OK, I suppose it is not that secure - but it could be better defence to key loggers than typing a plain text master password every time. Whether you think it is secure or not depends upon what you are trying to protect yourself from.
My problem is that I open and close Winscp several times a day and each time I have to type the master password. Lots of opportunity for a key logger to get access.