One idea that comes to my mind concerning the difference between the scripture and Dr. Eby's account of Stephen's vision has to do with the emphasis and the fact that the same event can be viewed from different perspectives. Since the scripture itself will sometimes address things from a "positional" perspective and at other times from a "practical" perspective, we have to keep this in mind. For instance, we are already positionally seated in heavenly places in Christ Jesus (Eph. 2:6), but in practice (practically) we are here on the earth attempting to "war a good warfare".

Perhaps in his comment to Dr. Eby, he was emphasizing the fact that he allowed Stephen to see him positionally seated at the right had of the Father: "to prove to his executioners that I was there". Since we could say that Stephen saw him "positionally seated" and in practice "standing", there isn't necessarily a conflict between the two accounts. He showed Stephen great honor by standing to receive him, no doubt with outstretched arms!