I'm 18 and have been working full time since I was 17. I work shift work at the moment, have done for the past 5 months (4am to 12pm) I have to get up at 3am to leave at 3:30am.
I can understand why your son wants to have a shower when he first gets out of bed, Generally people will have a shower before the leave to go to work to wake themself up abit, At 3am or even 2am in the morning it's cold and your body doesn't want to function especially after getting out of a warm bed, so a nice hot shower generally is required to get you motivated for the day. Also as said about the rules apart of HACCP in the food industry are quiet strict regarding personal hygiene etc.
The way the shifts are in our house goes like this:
Me: 4am to 12pm
Mum: 9pm to 5am
Ivan: 6am to 4pm
So people are waking up / leaving at different times of the day, yet we all seem to work together so that people don't disrupt anyone else's sleep patterns etc. When I first started this role, no one use to wake up when I left, However I did have a complaint from the neighbour across the road over my cars exhaust system being loud, despite the fact that I drive queitly at that time of morning. I got the exhaust changed anyway.
Perhaps sitting your son down and having a talk about his job and your job, plus what is required around the house and that everyone needs to help out. Explain to your son that you're curtious to him when he's trying to sleep as he should be to you. It's not that hard to be quiet around the house, you'll soon learn how to do things without waking someone up.
As to the "board / rent" situation - Regardless of whether you're on family payments or not and your son is working, You should discuss with him about setting up a board - I use to pay $80 a fortnight when I was 16 and my mother still got payments for me. Once the payments stopped it went up to $80 a week. Now I pay $150 a week, I've actually been paying rent for the past 2 months ($270 a week) To help the family out.
Also to get your son to help out around the house, prehaps try a different route in communicating with him, instead of saying "this is my house, these are my rules, you must obey them" or along those lines. Sit him down, talk to him about chores or jobs that he can do around the house that will help you and him both out. Give him some simple suggestions that he could do to help you out, He gets home alot earlier than you do so maybe suggest if he can put a load of washing on, vaccuum the house and explain that all these little things add up and help everyone out.
I just wanted to add, I don't think that you're being unfair in your requests - But knowing teenagers he's probably seeing it as some form of personal attack and doesn't understand what his actions are causing to the rest of the household. Again communication in a nice manner could really help this situation. I read above that someone mentioned that they got on better with their partners parents as they treated them like a friend instead of a parent - You stated that you're his mother not a friend. Maybe if you can bring those 2 things together, To be a mother and a friend to him he might realise what his actions are causing and might shape up to help you out and do the right thing by you.
Good Luck