From what is told in the summary, it seems like the software stack and these 3 people constitute the core of the business that is going on. The business may be something totally different. But it seems to be running on that software.
> And... $20m is revenue
Even if they have lower margins than what you yourself imagined, $20 m revenue/year is still a gigantic amount. You can improve upon whetever margin or inefficiency in the process and increase the net profit - optimize vendors, costs, sales pipeline.
The difficulty in modern Internet business is getting to some place at which you can command $20 m revenue from any market. Finding the customers and the users. Not the margins.
It’s not difficult getting to a high revenue fueled by aggressive and expensive acquisition using money from investors who gets dazzled by growth numbers, but if your customer lifetime value is low and you’re not a pure SAAS business which means margins won’t automatically improve with scale, turning that company profitable can prove very difficult.
Even before that, s/he doesn't even seem to understand any measure of business. $20m/year with 3 people is BIG. Any disturbance to whatever makes that happen will hurt the business greatly. When a full rewrite shakes the boat and causes a few millions of revenue loss or the loss of potential market share or opportunities, they will rightly fire him.
Best route would be to improve things without hurting anything. It doesn't matter things are 'properly done'. It matters whether the organization survives and prospers. What's 'proper' is redefined every 3-5 years, most of the time without objective basis anyway. So no need to hurt the business to force the current software paradigm.