That's right, in the H-1B context, there needs to be an employer-employee relationship between the petitioning company and the sponsored worker and this (in the eyes of USCIS) ultimately means the ability of the petitioning company to fire the sponsored worker and otherwise control his or her employment.
A CEO, CTO, CFO, CXO etc. are all "employees", technically an employee is someone who works for the company (unpaid work also counts) the company.
E.g. You can have 100% equity, be sole shareholder, pay money to a manager/employee to conduct work/business. You can even derive a dividend from the said business. however you cannot "engage in business" which means that you cannot write code whose IP gets assigned to the company. You also cannot have day-to-day management responsibilities. If I remember correctly planning a business and/or attending meetings of board of directors is allowed.
At end of the day shareholding pattern trumps everything else.
The problem here is if you are A, then no one will give 49% stake to you because of your idea. This only works on paper but in reality you will get screwed.