The 'not use every 3rd space' refers to trying to use a single-pole breaker in that slot which is fed by the wild leg thinking that it will provide 110V referenced to Neutral -- it doesn't. Is more like around 180V as I recall...

That said, using a 2-pole breaker for 208V single-phase is fine same as using a 3-pole for 3-phase power: You are now drawing power phase-to-phase in either case so it does not matter what slots are used.

As for can you draw full 400A from the wild leg, probably but if possible try to find out how your utility feels about it. Some will tack on a surcharge because their local grid was not setup a lot of people doing that. True full delta or Wye incoming service does not have any phase-to-phase load limitations but in turn in the case of delta require a transformer to provide building 110V service. Wye service is 4-wire with 3-hot legs and a center referenced neutral but generally have limitations to how much unbalanced single-phase (hot leg-to neutral) current is allowed.