Teenagers know everything about their life. Just ask them. They'll tell you you don't know them, that you're out of touch, don't understand them and their friends and the things they have to go thru everyday.
I've 5 kids. Everyone of them in middle school I've had to stomp such special snowflake tendancies just to bring them back to reality. I know this has worked for me because my 20 somethings aren't assholes and, like it or not, they understand their place in the world.
I suggest you do the same thing.
Tell him that not going to school is a legal issue. If you have made sure that he gets on the bus, and he is caught out somewhere, then HE will get the talking to by authorities. You'll get some too, but not as bad as otherwise. If you allow him to not go, then YOU will be the one getting the brunt of discussion from legal authority.
Second, here's my speech:
You're my kid, and in that way you're unique and I love you as my child, but understand something... You. are. not. special.
There is 350mn people in the US. Statistically speaking, all of the adults went to middle school, and all of the adults were 13. All of them battled with not being a kid anymore, weird hairs, funky new smells, wondering who is truly their friend and questioning how much school mattered to the real world. All of them sat at lunch and looked at the people at another table and wished they could have such good friends. The popular girl looked at the table of nerds and wished she could just have friends without all the baggage her friends have.
You don't think I know what's going on in your world? [here's where you relate a short anecdote of stupid shit from being 13]. I remember. And what I'm trying to do here is not as simple as telling you you're wrong. I'm trying to tell you what's best for you in 5 years when it's time to graduate high school and enter the real world.
Because the bottom line is this: Graduating high school gets you thru a doorway to the other side of a wall that cannot be passed if you don't graduate. You can get a GED, but employers and colleges see it much differently than a high school diploma. You can get to the other side, and into the real world, but not using that doorway by graduating HS will forever be a mark that people will see and think of you differently.
Of course, my speech is longer and more detailed, but this is the gist. You can fill it out as you need. But the thing that it needs from you is follow up, advice and wisdom on a regular basis. IOW it requires that you be an active parent, making sure that not only does the kid have direction, but they're getting answers to questions they didn't even know they had.
I believe that you'v tried all that you believe is possible or necessary. These were the palatable options. Conversely, it's still an option even if you don't like it. You're now left with solutions that will make everyone unhappy.
But if it means the difference between your 13yr old sitting in a Family Services office waiting for you to pick him up -- and the road that leads down -- or hating you for the next 2 weeks because you told him something he didn't want to or like hearing, yet he's in school, then which would you choose?