Phytohydra vs Trample
He still has to assign at least lethal damage to  Phytohydra before any remaining trample damage can be assigned to the defending player.  The fact that the damage will be replaced later on when it is dealt and not actually be "lethal" does not change anything about how it is assigned.  Toughness - Damage Marked (minimum, no deathtouch) goes on the creature, then the rest can hit you.


  702.19b The controller of an attacking creature with trample first assigns damage to the creature(s) blocking it. Once all those blocking
  creatures are assigned lethal damage, any remaining damage is assigned
  as its controller chooses among those blocking creatures and the
  player or planeswalker the creature is attacking. When checking for
  assigned lethal damage, take into account damage already marked on the
  creature and damage from other creatures that’s being assigned during
  the same combat damage step, but not any abilities or effects that
  might change the amount of damage that’s actually dealt. The
  attacking creature’s controller need not assign lethal damage to all
  those blocking creatures but in that case can’t assign any damage to
  the player or planeswalker it’s attacking.


Bold added by me