Moodle is certainly a great place to build and deliver the eLearning courses. That is Moodle's core functionality. Moodle can certainly control which students are allowed into which course, and features like separate/visible groups might be just what you need when people from different companies are studying the same course.
eCommerce is not Moodle's core functionality. There are some basic options for charging for courses, but your situation sounds like it may be more complex than that. In areas like this that are not Moodle's core functionality, Moodle is happy to integrate with other systems. For example using Moodle's Database Authentication and Enrolment plugins to connect to some other eCommerce system that handles the financial side.
Alternatively, if your volumes are small, at least initially, you might handle the billing and enrolment manually. That would allow you to be more flexible. Once you have got established, and worked out what procedures your customers would like to work to, then you could automate the billing.