Or, OS X could wait until the appropriate time to offer you the option of messing with your disk.
1. Don't ask about using the disk for Time Machine. When the user goes to Time Machine because they want to use Time Machine, then have a button in the sidebar "Use drive blah for Time Machine" for any non-time-machine external drives present.
2. Have a button at the top of a finder window in which icons have been re-arranged saying "preserve layout in this folder" (which you only have to click the first time, of course it remembers along with the layout). (Also, make it more convenient to default all folders/finders to list-with-details view, for people who have any idea what they're doing.)
3. When the user opens Spotlight, have a button in the sidebar "index this drive for Spotlight" for any un-indexed drives present.
In all these cases, it's still super duper easy to use all these things, without always bothering people who don't want these things.
1. Don't ask about using the disk for Time Machine. When the user goes to Time Machine because they want to use Time Machine, then have a button in the sidebar "Use drive blah for Time Machine" for any non-time-machine external drives present.
2. Have a button at the top of a finder window in which icons have been re-arranged saying "preserve layout in this folder" (which you only have to click the first time, of course it remembers along with the layout). (Also, make it more convenient to default all folders/finders to list-with-details view, for people who have any idea what they're doing.)
3. When the user opens Spotlight, have a button in the sidebar "index this drive for Spotlight" for any un-indexed drives present.
In all these cases, it's still super duper easy to use all these things, without always bothering people who don't want these things.