Good question. 除了 is a bit tricky, as is shown in your example. The 1st 除了，influenced by 也， is like "apart from" "other than" "beside". The 2nd 除了， influnenced by 都， is like "except".

1.He is here everyday. 2.He is here everyday,except Sunday.

The first sentence Besides Mondays, he comes here every day. The second sentence Except for Mondays, he is here every day.

Meaning: He come here/be here all days except Sunday.

1.He usually comes here except Sunday. 2. He always be here except Sunday