The key here is to understand what exactly is being done with the Matanos. It would seem that after dipping the finger in the blood it would spread all over the finger and therefore could not be effectively placed on the corners of the Mizbe'ach. Bending (this is Rashi's translation) the thumb and small finger onto the Etzba will enable the Kohen to control the blood on his finger and direct it towards the corner. This is basically the reason for using these other fingers, based also on the Rambam's explanation (Hilchos Ma'aseh ha'Korbanos 5:6).

The same two fingers (thumb and pinky), however, serve to do the Kemitzah (Menachos 11a) and to push the mixture of flour and oil into the Kohen's hand, so this is proof for the Rambam's reasoning that using these fingers helps control and direct the blood on the Etzba.

Yoel Domb