For me, "at" still translates to "and" in those cases. I think the "problem" has to do with the way we form such sentences. In the correct order of things, the cause always comes before the effect. However, when we say such sentences, we talk of the "effect" first and follow it with the "cause" and with that order, the English translation would now differ.
So, in "mabuti at magkakasay tayo", which can be translated to "it's good that we are riding together" (effect-cause), if we'll transpose that to the cause-effect sequence, that will become "we are riding together AND it's good". "Masaya ako at dumalaw kayo" translates to "I'm happy that you came to visit" (effect-cause), again, with cause-effect arrangement, "you came to visit AND (for that reason) I'm happy".
Let's just say that we put the cart before the horse in such sentences, but the "at" would still mean "and".
BTW, are you sure the word is "magkakasakay" and not "magkakasabay"?