No... the new APIs take over all monitors. When you use the fullscreen apis, you can then target your windows for the other monitors. No body does so you see crosshatch pattern on them. If you download final cut on MAS and fullscreen it will use both monitors.
The problem is that fullscreen gives developers all monitors because the feature is supposed to encompasses the user entirely in one app experience, throwing out the multitasking concepts. It's like distraction free mode in many editors and follows the iOS concept of one App at a time. Apple allows the developer to use all the monitors when in fullscreen the way they want in the app but less than 5% of the fullscreening apps actually do anything with the other monitor. This unfortunately isn't the pattern that many users want especially when less than 5% of the fullscreening apps do anything with the second monitor mostly using the full screen mode to help 11 inch MBPAir users effectively use space.
Given that, fullscreening windows without the Apple API (as was done in older Mac versions) will still work but it's tricky and many apps didn't behave perfectly. The new API while not perfect is simple and just works for most devs, so they use it.
The problem is that fullscreen gives developers all monitors because the feature is supposed to encompasses the user entirely in one app experience, throwing out the multitasking concepts. It's like distraction free mode in many editors and follows the iOS concept of one App at a time. Apple allows the developer to use all the monitors when in fullscreen the way they want in the app but less than 5% of the fullscreening apps actually do anything with the other monitor. This unfortunately isn't the pattern that many users want especially when less than 5% of the fullscreening apps do anything with the second monitor mostly using the full screen mode to help 11 inch MBPAir users effectively use space.
Given that, fullscreening windows without the Apple API (as was done in older Mac versions) will still work but it's tricky and many apps didn't behave perfectly. The new API while not perfect is simple and just works for most devs, so they use it.