The vertices of a snub cube form a metric space with 24 points that is homogeneous but not bihomogeneous: the edges of the squares have a "direction" associated with them.
Added later: here is an example with just 6 points: take an equilateral triangle with sides of length 1, and take the 6 points on the edges that are distance 1/4 from a vertex.
Added later: There are no examples with less than 6 points; for example, for 5 points there are 10 edges so there are at most 2 possible lengths with 5 edges of each length, which gives essentially only 1 configuration and this is bihomogeneous. Less than 5 points is easy to do case by case.
