It probably didn't make as much of a difference during Moonlighting's original run, when long stretches of reruns were already enough to sufficiently disrupt continuity between new episodes, but it's a whole different ballgame when viewing the series in sequence (on DVD or otherwise).
I LOVE "Atomic Shakespeare", hate "Wonderful Job", and am ambivalent (as Maddie would say) about "The Straight Poop"... but regardless of this range of reactions, I feel that all three in this "trilogy" of alternate universe episodes should be skipped when watching the series in order and saved for their own occasions (although I personally would be fine if I never see "Wonderful Job" again).
After the absolute magic of "Mulberry Street", it just seems wrong to shift gears so completely with three consecutive off-the-wall episodes that ALL include scenes of Bruce and Cybill (regardless of who they are portraying) passionately making out. It distracts and detracts from Maddie and David's brilliantly crafted, gradually building relationship just as things are ramping up.
You know what? The more I think about it, the sprinkling in of reruns "back in the day" probably helped to maintain the sense of a logical progression in spite of Atomic/Wonderful/Poop before everything would change forever.