OP: "... Unfortunately this doesn't give the same functionality as opening a file directly in ACR flattens all layers ..."
Actually, the only file formats that the external, directly called version of ACR can read are raw files (which are obviously non-layered), JPGs which have only one layer, and single layer TIFFs. It doesn't flatten anything -- it only reads single layer files. In fact, think about it: the "internal" version can only work on one "layer" at a time, too.
IMHO, because the external version of ACR can read hundreds of different raw file formats, and because the conversion process is not at all trivial, most people would say that the external version of ACR has quite a bit more functionality than the recently introduced "internal" version that can be used inside of PS to act on a layer.
To illustrate how much more capable the external version is, do a little experiment. Take a picture at night under pure tungsten illumination, say, your living room. For yucks, crank up the ISO setting on your camera to 1000 or so, but still, accidentally-on-purpose (LOL) underexpose the shot by a stop or so. To give ACR a good workout, set the on-camera white balance to "daylight", not tungsten. Save it as a raw file.
Next, make 2 identical copies of this raw file. Give each a different file name. Process the first copy in "external" ACR the way you normally would process a raw file, e.g, adjust the white balance, exposure, contrast, noise reduction, etc., and then save the result directly from "external" ACR as a JPG.
For the second copy, also pull it into the "external" version of ACR, but this time, just use the default (ie, everything zero'ed) settings, but then export it into PS, and attempt to adjust WB, exposure, etc. within PS using the "internal" version of ACR. I think it will be pretty obvious that the "internal" version of ACR simply can't match the abilities of the "external" version of ACR. The WB won't be as good; for a given amount of NR, less detail will be preserved, etc.
Because of it's ability to process a huge number of different raw file formats, and it's ability to give substantially better results is why I simply can't agree with your statement that "external" ACR has less functionality than "internal" ACR.
Cheers,
Tom M
PS - It looks like Mr.T was absolutely correct when he observed that the "Snapshot" tab is not available when using the "internal" version of ACR (ie, as a PS filter, not a pre-processor). I tested it in the three versions of PS I have on my machine, and the "internal" version never displays the "Snapshot" tab.