I think currently the goal is setterm, keyboard rate and numlock to be set by kbd (notice that console-tools is also obsoleted) and font & keyboard layout -- by console-setup. It is not difficult for console-setup to take control on these too but I am not sure about the advantages of this (except maybe that the keyboard rate can be shared with X).
Regarding the 2 config files and the user not knowing which one is going to win -- I think you are right. I think we can add a Debconf menu similar to the one the user gets when he installs together several desktop managers (xdm, gdm, kdm and wdm).
----- Original message -----
I think there are a few things that console-setup doesn't do
that atleast console-tools does:
- calling setterm to set powersaving mode.
- Set keyboard rate
- Being able to set numlock on boot
Anyway, my problem with the current situation is that there are 2
config files where I can set the same thing, and it's not obvious
which of the 2 is going to win.