I'm thinking of putting a Seymour Duncan lipstick tube pickup (RW/RP) into my strat in the middle position, for a surfy 1960's tone. When playing the strat in positions 2 and 4 will it still keep that out of phase 'stratty' sound or sound different?

It'll still sound pretty Straty. In fact, the lipstick pickups is pretty boomy, you'll probably get a thicker 'quack,' if that makes sense. Odds are that'd be great for the sound you want, though.
It wont be quite the same, but you might want to check out youtube reviews of the Richmond Belmont, which has a SD '59 humbucker in the bridge and SD Lipsticks in the neck and middle positions to get some insight.

You might also check out Tesla's Lipstick pickups as well.
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