Is it idiotic to stack an amp and tuner directly on top of a CD player?

Whipsaw - I like hifiman's suggestion to try the Herbie's Tenderfeet in your non-ideal arrangement.  The owner's manuals often recommend a minimum amount of space around a given piece of gear.  I doubt you will get that space even with the larger Tenderfeet but at least check what the recommendations are.   Be that as it may,  if it were my gear, I would NOT put the amp on the bottom.  That's the piece that likely needs the most ventilation and in that bottom position will also be serving to heat up the gear above it - even with the air-space provided by the Tenderfeet.  If worried about too much weight on the CDP, I'd go with Amp on top and CDP in the middle position.  Use the corners of the CDP to position the Tenderfeet since the case corners will be the strongest "load point" and possibly have adequate rigidity to prevent the warping someone cautioned about.