I guess you added the condition of having a username/password in the form to activate Kee because it would fill any field in any page elsewhere. The note on TOTP in placeholder documentation is very helping by the way.
To manage the lists I would say that optimally, Kee should fill the forms as soon as there is a corresponding entry for the webpage and one of the field name or id specified in the KeePassRPC tab appears in it. It solves the current problem which is that you have to write the field name/id two times : in KeePassRPC and in Kee whitelist. According to me, if you write it in KeePassRPC and enable placeholder it somehow means that the user is already aware about security issues and rare bad filling attempts. Maybe you can find a security issue in my argument because I am not really well aware of everything.
Also, it could be very nice to have a field selector as in KeePassHttp to complete the KeePassRPC without the inspector (but yeah, lot of work, it can wait)
I bet all of this is a really big work given the time you have and that maybe you have to rewrite some core part of Kee. So if you lack of time, maybe you can improve the presentation of whitelist in Kee for now.
I think that you should use a textbox rather than just a big line to show what fields are in the list, we can’t see currently entirely the whitelist in one look it is really annoying.
You can index the list with the output of the field : one whitelist for username, one for password, one for otp … without changing anything in the current field management ! It just allow to structure the different parts and remember what this field is for (in the global whitelist especially).
And you should give the user to add output type as before in the list and filling it with the good fields name/id.
Hope this help !