A few notes: 1) As the Maharsha and others point out, there are in fact many sources that attribute the mitzva of אותו ואת בנו to compassion on the animal. The specific question of Tosfos is that the Kalir instituted it to be said by the שליח ציבור during שמונה עשרה, which is precisely what the Gemara forbids and tells us to silence such a person! 2) Now that we have the full text of the קדושתא, it turns out that מחשבותיך לרחמנו is in fact an entirely unrelated phrase, designed to link the last word of the last pasuk (מאוד עמקו מחשבותיך) to the conclusion of the bracha. 3) Even on Rosh Hashana, we do in fact include מעין החתימה סמוך לחתימה by adding the words מלך עוזר ומושיע ומגן after זכרנו. In its original form though, the מעין החתימה of the Kalir substituted מלך עוזר...