I reckon that he'll get into a good routine/his body clock will get sorted soon enough. It probably isn't helping that sunrise is later and later. In our house (even though me and DC 19 and 13 are early risers), we have the Hue lights that are timed to switch on (they do a sort of "sunrise" thing), plus multiple alarms (on phones, Alexas etc!!). This works for us.
I'm a nurse (so shift work is the norm!), but from Y6 primary, my DC had to get themselves up and ready for school (and my eldest for work now) due to me having to leave for work just after 6. I taught the DC to get stuff ready the night before, go to bed at good time etc. In the morning, you're up, washed/dressed, beds made, cats fed, litter scooped, breakfast dishes washed up etc. They would leave house in time with correct uniforms and packed lunches. That seems to have stuck with them. I do still pop my head around their bedroom doors to say hello/goodbye/make sure all ok before I leave. I don't think it's unreasonable to help in short term while he gets body clock back in sync, and gets things like alarms etc sorted. On my days off, I tend to wake early anyway, so it's not a hardship to pop my head around their doors (but they are up anyway).
Logistically though, it seems like an awfully long commute, and depending on public transport can be trying (I remember it well!). How far away is his work from where you live? I know your son can't drive yet but can he get CBT done and kit himself out with a 125 moped (and the safety gear) to get himself to/from work? Or a (UK LEGAL!) ebike? Do you have a safe place to store this sort of thing at home? Is there a safe place at work to lock a motorbike or ebike?
I have a car license but I tend to use my bike (motorbike) or ebike (it's a Tern ebike, completely legal and insured). DS has a 125cc motorbike that he uses for getting himself about: he got his CBT at 17 (and renewed it last month). I paid for his provisional license, his bike gear (I insist on full protective gear for myself and the DC when they are riding or are pillion on motorbikes) and first CBT. And I set him up with a moped to get road experience on and the first year of insurance/MOT/tax. He then spent 6months saving up for his 125cc bike (and pays for it's servicing, insurance, tax etc). He's working towards getting his A1 or A2 license. I've got my bike, DD wants to ride too (but is too young currently). Goes without saying, that DS knows that having a license is a privilege, not a right, and any nonsense (or him sodding about being unsafe or breaking the law) means I'll take his keys and report him myself.
Costs of motorbikes (buying and running costs) are lower compared with cars. £29 for MOT, £20 for tax, £10-20 to fill up. MPG is good. Insurance will be higher when they first start out, but I think still cheaper than car insurance. I bought DS first moped for £700. Boots, trousers and jacket with armour, helmet, gloves, and high vis waterproofs for wet weather/night riding probably £600 tops (but you can shop around). You can buy secondhand for most wearable gear aside from helmet, so that saves some money. At home, we have ground anchors, Sold Secure Diamond rated security chains, locks, bike covers= vf etc.
Of course, there are inherent dangers on the roads with both cycling, motorcycling (and driving cars), but careful/safe riding, being aware of surroundings, wearing protective gear etc is the way to go. I didn't get my car license until my late 20's, so most of my life, I've used cycling as my main transport. We're in a village and transport links aren't TOO BAD....but still a lot quicker/cheaper to use motorbikes or even cycle for our work commutes, compared with the buses.