thanks for your reply.
About shared accounts between UE and UC, I tried that some time ago (1-2 years), and I remember I had to revert back to split configuration because of some issue I encountered (but can't remember exactly what ...). I'll give it a new try, this may have changed (but won't solve them main issue though).
Can you tell me more about "It is further possible to save password / passphrase in the settings of an FTP / SFTP account"? I know how to store the password for a user account, but I can't find anything for the passphrase of the SSH key.
About your last suggestion, yes, PAGEANT loads the private key(s) that you want and will pass key(s) (along with the passphrase(s) I guess) to the tools that can work with PAGEANT.exe. This is the case for Putty, FileZilla, Sublime Text, NotePad++ (using plugin NppFTP) and probably many others. I tried to configure the private key in "PAGEANT format" in a test SFTP connection but PAGEANT.exe did not seem to "catch" the key and be able to "send" the passphrase to UE/UC because UE/UC asked me for the passphrase anyway.
I had a look at the link you posted (Howto use Pageant and Putty). Real life is simpler than what this page describes : run pageant.exe at windows boot with private key(s) file names as parameters, enter once the passphrase(s) when prompted to (after windows boot) and that's pretty much over : Putty, FileZilla, etc. will never again ask for a password and use the private key instead (without typing the passphrase).