Where is the source that kiddushin should be made in this manner? I understand the Gemora uses it all over, but is there a mekor that it should be this way? Do we find anywhere else that a Biblical mitzvah should be done subject to the will of the Rabbis?
Thank you,
Avromi
(a) It seems that this is a Sevara that a person should want to carry out Kidushin in a way that fits in with the Rabanan's intentions. In addition Chazal also wanted people to perform Kidushin according to their Halachas - because otherwise they could not annul Kidushin in certain cases where it was necessary to cancel them, as in our Gemara for instance. Therefore Chazal instituted that one should say "k'Das Moshe v'Yisrael" at the time of Kidushin (as Tosfos writes) because then if someone says afterwards that he did not do the Kidushin according to Rabanan's wishes, we can say to him that "Devarim shebe'Lev Einan Devarim" - the crucial thing is what he said not what he thought (see Ritva).
This idea seems to be hinted at by Shita l'Ran who writes that the Gemara means that a person wants the Kidushin to be valid according to Chazal's will. It depends on their will, not only on their da'as.
(b) (1) I found that "Tziyunim l'Torah"(Rule 23) by Rabbi Yosef Engel zt'l discusses your question. He cites Tosfos Kesuvos 106b DH v'Ki that when somebody makes a donation to the Beis Hamikdash he does so according to the Da'as of Beis Din. Since "the heart of Beis Din makes conditions" it follows that the intention of the donor is consistent with that of Beis Din.
(2) R. Engel also cites the Kli Yakar (Bamidbar 30:3 DH Lo Yachel) who cites Chagigah 10a that the person who makes the vow cannot annul it but others may annul it. We derive from this that a Chacham can annul a vow. The reason is because every Jew is in the auspices of Beis Din and is obligated to do everything that the Beis Din instructs him. Anyone who makes a vow is as if he made a condition at the time of his vow that he is only doing so if Beis Din will agree with him. If the Beis Din does not agree the vow is uprooted right from the beginning.
(3) I also found that the Chazon Ish YD 196:14 writes that the Din concerning Chalah in the Diaspora - that one may eat and afterwards separate the Chalah - applies because the Beis Din made a condition that immediately after the dough becomes obligated for separating Chalah, the piece of Chalah which later will be separated, becomes Kodesh already. Since Chachamim fixed this Din it became a fixed institution for all of Yisrael and therefore all of Yisrael must do according to the Chachamim.
A Gut Yom Tov
Dovid Bloom