Also why did the Github owners agree to be paid in Microsoft stock instead of real money?
I think it's safe to say that Microsoft offered them a much lower price in cash (potentially billions lower), which is why they went for the stocks.
It's actually a very smart move from Microsoft with how its stocks are hovering around their all time high levels, where in current state of the stock market, a correction might be due. In other words, Microsoft wisely hedged a potential downfall of its own stocks by acquiring GitHub. By the time the stock market correction has taken place, they will buy back their stocks at much lower levels. It's a game that's being played, where the wealthiest always have the main advantage.
It's basically the same as when you try to sell your car to a dealer. Cash value is always lower than trade value.
There might also be arrangements in the deal for when and how much the sellers are allowed to sell the stocks hehehe.
Definitely.