Depends on if you're doing the 3 days a week thing because of actual time commitments or if you're trying it because you heard it's supposed to be "all you need" or "better for mass" or something.
Generally speaking if you got your deadlift to an actual 500 on 5/6 day a week programs, I'd stick with 5 days a week unless your schedule actually prohibits it or you just don't feel like that any more. Your hunch is most likely correct in that you feel better on 5/6 days and you've got more faith in those routines.
Not that you CAN'T get the 3 days to work, just that's not what I would pick personally.
As for a 3 day/week routine, the one you posted is absolutely no good. Good Lord no. You don't need both the variations of bench press 3x a week each.
Better 3 day/week program would be something like:
Military press, strictly no legs
Bench OR incline bench
lower body emphasis: pick 3 lower body exercises (only one can be a deadlift variation).
Upper body emphasis (pick 2 back exercises and 2 shoulder/arm exercises. NO more benching today)
Seated overhead press from pins
Whole body conditioning: Pick 3 exercises that hit every single muscle between them and then do them in a circuit. Mix med ball throws or jumps between the 3 exercises (example: 1) dumbbell row, then med ball throw against a wall, 2) walking lunges, then jumps, then 3) farmers walk.)
Still, all in all I'd much rather do a 5 day program myself.