Hi,
Thank you for the precision 
I agree that if a clipboard logger is running on your computer then it should not be the only running malware.
What surprise me is that on the one handKeePassRPC allows a safe communication between the softwares in local to prevent generic malware running to get everything from KeePass’ data base and on the other hand Kee uses clipboard for generated password which is a vulnerability against a generic software like clipboard logger. Of course, you generally use passwords everyday (which is safer thanks to KeePassRPC) and you rarely change your passwords (this is the weak part), but still, I was wondering if something was planned to avoid this weakness since everything else seems so high in security. I looked at password managers only recently, so if you tell me that we are already to the point where everything is compromised when a clipboard logger is running then I can only accept this little weakness.
In conclusion I would say that if you use Kee to fill form on a compromise PC (by a generic malware) KeePassRPC may avoid that passwords used were leaked but if you generate a new one with Kee on the same PC then it was leaked if there is a clipboard logger running.
And as you said a solution to avoid that is to go back to KeePass and create/change entry there (less practical but safer).
Yes, you have to complete the procedure before doing anything else and with enough charge as you pointed out !
Thank you again for your answer and your very nice work 
Best !