Quick recap... Apple was suffering when the IBM PC's came out because Apple inisted on proprietary connections, accessories, etc. Steve Jobs was kicked out and the company barely held on thanks to some support from the educational market. Microsoft realized that Apple is a good innovation company (and therefore would keep MS on it's toes) and injected Apple with a huge wad of cash for the "rights" to develop Office applications on the Mac OS. It was pure charity really - MS did not need to do this.
Then Steve Jobs came back with a whole new mindset, but you can see Apple's insistence on propietary technology continuing in the iPod/iPad/iPhone lines.
I think you missed a lot of reality.
In 1997 when Steve Jobs returned, US$150 million was not a huge wad of cash to Apple, which had $5 billion in the bank and no long term debt. Microsoft's promise to continue MS Office products was more important to the industry using Macs than the pocket change. Apple's stock price was up from a lot of about US$13.50 per share in 1995.
Microsoft made more profit on each Mac product than on the same product for Windows. They wanted that revenue stream to continue. They could also try new things on Macs before doing the same thing on a larger scale on Windows.
Back around 1986, Steve Jobs left the company after he, Steve Wozniak, and the board hired John Sculley from PepsiCo to work the company financially. Steve Jobs and John Sculley did not agree and Steve Jobs went on to found NeXT, Inc., a company manufacturing and selling UNIX-based computers.
John Sculley helped Apple financially and killed off innovation, except for the Newton Messenger. After he was removed, Michael Spindler drove things into the ground. They finally got Gil Amelio, who turned around National Semiconductor to run the company and Ellen Hancock to re-work the technical side. They bought NeXT, Inc. and Steve Jobs.
They put Mac OS and NeXTStep together and Steve Jobs introduced the iMac in 1998, which had already been in planning before he arrived. Mac OS X arrived in 2000 as a public beta.