We took the Ancient Kingdoms trip last February, and we think the OP's original cautions regarding the physical requirements of the trip are somewhat overstated. Except for ankor Wat and Ankor Thom, we did not find the walking overly exerting or difficult. And only in those two locations because of the heat. Nor did we find that boarding the boat for the Mekong River transit from Vietnam to Cambodia to be difficult either. We will opine, however, that it was one of the best trips we've taken, without a doubt. Expecially if one takes the post-trip extension to chaing Rai/Chaing Mai. the visit to the hill people as well as the elephant ride through the jungle on that extension were, in our humble opinions, among our trip highlights.
As far as visas are concerned, we can state with certainty that you can get a Cambodian visa at the jungle checkpoint, because one member of our group failed to procure this visa in advance, as suggested, and had no choice. He was indeed accommodated at that checkpoint, having the visa issued after every other boat was processed, which had the effect of holding up our entire group for about three hours. Waiting in the heat for three unnecessary hours, did not endear this traveler to the group, and the results were discussed elsewhere. Our advice: Be a good citizen. Get this visa in advance. In fact, get all your visas in advance.