What is the legitimacy of a supplication asking for forgiveness for rejecting a truth that the mind could not comprehend or the heart and innate disposition could not accept, and for rejecting a truth that was perceived as false and for which no proof was established, and asking for forgiveness for not entering into a certain religion or madhhab if it was indeed true?

There is no objection to the first two paragraphs. As for the third paragraph, this supplication is not permissible, because the true religion accepted by Allah is Islam. Allah Almighty says: "And whoever desires a religion other than Islam, it will never be accepted from him, and in the Hereafter he will be among the losers." Therefore, the concept of truth is not accepted in a religion other than Islam. As for "such-and-such a madhhab," if you mean a jurisprudential madhhab, then there is no objection to it.