" the toothpick in the hole with the bottom of the flipper resting on it" That's for Bally/Williams, that doesnt work with Data East/Stern playfields - the hole is supposed to be in the dead center at the tip of the flipper bat.

The best alignment is as you said in the second part: in line with the inlane, an extension of it. (not for Gottlieb Sys 3 though, they are meant to droop a bit, in line with the biff bars)