These two sentences can have the same meaning: I agree with you, but the first phrase is more usual. However, the sentence " je m'accorde avec toi" can have another meaning if you add an object: "je m'accorde du bon temps avec toi". Here the verb "accorder" means "give yourself sth".

For me, even if "je m'accorde avec toi" don't sounds very well, I understand Je suis d'accord avec toi: I'm agree with you Je m’accorde avec toi: for example, if you and your friend have to make a choice he can tell you this sentence, which will mean "Choose and I'll follow your choice". I don't know if I'm understandable. In the first sentence, he is already agree with you, in the seconde he will adapt himself at your choice.

"Je m'accorde avec toi" sounds weird to me, I prefer "on s'accorde bien" (we get along nicely). So "je suis d'accord" as a totally different meaning, it means "I agree with you", it's about something precise (opinion on one subject) whereas "s'accorder" is generally been comfortable with someone.