Hide the Windows taskbar while a game is running: This option is intended to make the transitions between PinballY and running games more seamless, graphically, by making sure that the Windows taskbar doesn't pop into view during game launches or when games are exiting. This option simply hides the taskbar entirely any time a game is running.
The reason this is optional is that Microsoft doesn't consider it good practice for applications to mess with the taskbar like this. The taskbar is supposed to be the exclusive province of the Windows desktop. In this case, though, it's somewhat justifiable, as PinballY effectively serves as a replacement for the Windows desktop as long as you're operating in "pinball mode". If you have any problems with the taskbar remaining hidden after you exit PinballY, or anything along those lines, disable this option to make PinballY behave itself with respect to the taskbar.
Terminate game when idle for (seconds): This sets an inactivity timeout period for launched games. If you launch a game and then walk away from the system, not touching any buttons for a while, PinballY will terminate the game and return to its menu display when this timeout period expires. Set this to zero to disable the timeout entirely.
The timeout won't kick in while you're actively playing a game, since it only takes effect when you haven't pressed any buttons for the timeout period. So it doesn't limit the amount of time you can play a single game. It's just there in case you walk away from the system while a game is running, to ensure that the system eventually returns to "attract mode" if left idle for a long time.
"Keep the following windows open...": These checkboxes let you tell PinballY to continue showing one or more of the PinballY windows when any game is running. The selected windows will remain in the foreground and will continue to show their background graphics or videos throughout each game.
Normally, PinballY blanks all of its windows while a game is running, and allows the running game to place its windows in front of the PinballY windows (to the extent they're situated in the same display area). The assumption is that you want the game to take over the entire display while it's running, and that you don't want PinballY wasting CPU time and video memory by continuing to play back videos in windows that are covered up by the running game.
However, you might want to keep some of the PinballY windows open while playing some or all games. For example, none of the current player systems provide their own dedicated instruction card window, so if you have a physical monitor area that's suitable for an instruction card display, you can tell PinballY to keep its instruction card window active during play, by checking the Instruction Card box here.
When you set a window to continue showing graphics while running, PinballY also forces that window into the "topmost" window layer on the monitor while the game is executing, so that the PinballY window stays in front of any window the game itself displays in the same screen area. This is an attempt to ensure that the PinballY window not only fills in for missing game graphics, but actually replaces any graphics the game tries to display in that screen area. The idea is to let you replace any game graphics that you don't like with your own custom images or videos. For example, some systems make a half-hearted attempt at backglass graphics by displaying a static image with no animation. You might prefer to show the PinballY backglass video throughout play instead in such cases. The automatic "topmost" layering helps ensure that the PinballY window will appear in front of the game system's window, effectively replacing it on the screen. (This isn't absolutely guaranteed to keep the PinballY window in front, because the game could also lay claim to the "topmost" layer, in which case it will usually have precedence because it's the foreground application. You might need to resort to tweaking the game's settings in such a case to tell the game not to show the unwanted window.)
The settings here are "global", meaning they apply as the defaults to all games. You can also control which PinballY windows remain active on a per-system and per-game basis. If you want to select a set of windows that will remain active during play only for games of a particular system, you can do that using the player system options page for that system. Each system's settings page has its own set of the checkboxes shown here where you can make the same selections for that individual system. The settings for a system override the global settings here. Similarly, the Game Details dialog has its own set of these checkboxes, where you can override both the global settings and the system settings.
"DMD" vs. "Real DMD": The DMD checkbox refers to PinballY's on-screen window where it displays DMD-style graphics. The Real DMD checkbox refers to your physical DMD device (such as a PinDMD or Pin2DMD unit), if you have one. The Real DMD isn't a window, but the same principle applies: if you check this box, PinballY will continue to show its image or video media on your real DMD device while the game is running. This will prevent the launched game from displaying anything on the DMD, since the real DMD devices only allow access from one program at a time. (In some cases, a game that tries to access the device might detect the conflict and show an error, or exit abruptly, or even crash, so it's best to use this option only with games that don't try to access the DMD device themselves.)