I don't have hard sources on Harmonix keysounding and may have misremembered things[0], or this might just be community misinformation. The article you are linking to concerns Guitar Hero III, which was made by Neversoft after Activision bought RedOctane
without Harmonix. At that point they had enough money to pay for patent licenses. The amount of money being spent on guitar games in the US was
utterly insane at this point (and part of the reason why they died off so quickly).
A few years prior they did NOT have that kind of money. The history of Guitar Hero is that RedOctane was involved in manufacturing third-party softpads for people importing DDR home games from Japan. They saw GuitarFreaks in a Japanese arcade and contracted Harmonix to build a game around a guitar controller. The game they made, Guitar Hero, was startlingly low budget, with loads of covers[1]. Nobody had any money to license patents.
In terms of the cost of actually keysounding a track, relative to Harmonix's patent workaround... I'm not entirely sure. It could go either way. I could imagine some automated/cheap way to do 'good enough' keysounding could have been made, especially since they're already charting out note data.
[0] For example, I said Harmonix was involved in the ITG lawsuit but it was actually RedOctane who published ITG. I'd edit my comment but I can't find the edit link.
[1] Which arguably worked in the game's favor - I do remember people noting that the all-masters-all-the-time approach of Guitar Hero World Tour made playing vocals feel strange.