The only way to have 5 ranks of lowered pikes is to have all the ranks with the lowered pikes as well. This is because the vanilla phalanx only has 4 types of ranks (1st rank in knees, 2nd rank in normal stance, 3rd rank with overhand pikes and back ranks). The 3rd rank only appears in guard mode. We could make all ranks get their spears down to greater effect as stopping power, but it wouldn't be realistic, as I can't imagine more than 5 ranks having their spears lowered without hitting some companions in the front ranks or without messing up the formation. So, in EBII we use only the first 3 ranks.

As for penetration power, all units can eventually get into close range, but their first impact will be minimal. They can only penetrate by slowly moving through the pikes. Exceptions exist of course: other phalanxes and most notably elephants. The large Indian elephants can penetrate the phalanx more or less easily, although a concentrated mass of pikes can make them stop and get killed. So, you know the drill: get the elephants in front and break through the phalanx, then charge with swordsmen units to prevent the phalanx from reorganizing, then hit with a cavalry charge in the flank. Of course, this is theoretical, because a good adversary will deploy javelinmen in front and sides of the phalanx and kill as many elephants as possible and guard the flanks with spearmen and rear with swordsmen, to protect the phalangites' retreat when the melee starts.