So the sentence, 'He goes to church sometimes if unusual', is just a nonsense?
How about 'He sometimes, if not usual, goes to church'?
I saw a sentence, 'He seldom, if ever, goes to church' .And I tried expressing a sentence meaning 'He sometimes goes to church, though it's unusual', using 'if ' instead of 'though'.
Yes, it is. You could use your second suggestion - but you will need "usually".
However, neither exactly expresses the meaning of "if ever", which really means that "he probably never goes to church". His chuch-attendance is so rare that the speaker cannot really recall him going.