before you think about starting your own business in chemistry you should probably see what its like to work in a lab. You rarely sit down in deep thought for days on end without getting anything done in your hood. If you're talking about the industry it depends where you work. Most places in big pharma or biotech are going to expect you to work an 8-9 hour day. Some companies have a harder working atmosphere though and you're expected to work 10-11 on average and when you have a deadline to meet you might be burning the midnight oil. Some places actually have a "productivity police" atmosphere and some are more relaxed. I've heard of places where people check each others notebooks to see how much work was done. I work at a place right now where they worry more about the hours. If you start your own lab though you can bet your ass you're working way longer hours than anyone else.
To answer your question its not likely that anyone reprimands you for showing up an hour late one day with a good report (when you're meeting the deadline). Nobody punches a clock in biotech/big pharma. People will keep an eye on if you're around the lab and stuff but as long as you get work done in a timely fashion its OK.
I wouldn't get worked up about being trapped behind a degree either. If you stay in science you can move around. After all your BS education is only 4 years of a 40 year career. It's not going to define your career.
If you want to start your own lab you should also keep in mind that you're responsible for far more than just science. You need to keep tabs on accounting, make sure you're up to code, with the eh&s,..etc. Those things will all take time out of your lab time.