Funny you should ask about this. One of my professional clients called me about their practices yesterday. They run a 20 bbl system and the tun doesn't have rakes. They have a vorlauf pump, but had not been using it until the end of the mash. I recommended that they perform more recirculation during the mashing to improve the overall mixing of wort within the mash.
You can either move the media or move the liquid. Most homebrewers can mix their mash. But when you get into the 20 to 200 bbl range, its tough to mix the mash unless there is a built-in raking system. However, we RIMS brewers know that mixing is not necessary since we are moving the liquid.
In my opinion, you should sample for pH after you have mixed the mash well and vorlaufed any foundation water from the bottom of your tun. Remember, that water is part of the overall chemistry of the mash system. Your sampling should make sure that is well incorporated in the overall wort.