‘at the company’ is a natural alternative to ‘in’. Both are ok, but I’d say ‘at’

Both are perfectly correct and natural. I don't think there's any difference at all in meaning. A native speaker might choose one or the other depending on flow, context, and what they want to emphasize. For example, if the following sentence was about numbers of employees, they might choose the first form: "The company I work for has forty employees. Over half of them have been with the company for more than ten years."

Both correct You could also say that the company employs 40 people.

You can say either. They're both grammatically correct.

"The company I work for has 40 employees" and "There are 40 employees in the company I work for" Both are correct. Good luck!