Picture a four-dimensional space (x, y, z, t). Picture “a single point” (let’s call it (x, y, z, 0). Is that single point within the framework of the 4-D space? Why yes… yes it is. QED.
It was energy. We can’t get to what it was prior to that, if anything. The universe expands at the point of the Big Bang (and has continued to expand). That doesn’t mean that it didn’t exist at the time of the energy->matter transformation. At that point, we have physical extension (if only at a point).