Probably, yes. Qubes bind-dirs will become available in Qubes R3.2. (And that should come out “soon”. (?)) (Up to you if you still want to invest energy into the old Whonix bind-directories.)
Yes it has no config at all. Can only be edited by changing it directly.
One one hand, i2p is supposed to connect in the clear, you cannot configure it to use Tor as a proxy or force it by using a socksifier. So it will use system DNS. But on the other hand, Whonix-Gateway by default does not provide any kind of system DNS, torified or not. You could enable torified system DNS, but that of course would require editing and a functional /etc/resolv.conf. I see no way around that. Unless you can teach i2p to somehow not require DNS. Or somehow only allow torified system DNS for i2p and blocking system DNS traffic for everyone else.
(For completeness sake only: would also be possible to modify Whonix-Gateway to a point where it does clearnet system DNS but I guess that is besides the point here.)