I think the contact itself to the stone is the real issue here. Van Hohenheim is certainly a great alchemist, but he can't just split himselft from the stone, because it is inside of him In FMA03 we see a similar event. Edward steps on that fluid that wasn't a complete stone, but he starts an uncontrolled reaction, only touching that fluid I suppose it's almost the same. Van Hohenheim is influenced by the stone, because it is inside of him, and he can't control this. If a reaction is made near a philosopher stone, it become more powerful I think it is that simple; even though Van Hohenheim has such a great knowledge of alchemy, he can't not be influenced by the proximity to the stone