Chris Miller said:
Thanks for sorting through my poor phrasing to understand my question, and for the more exact thought experiment. So, because both clocks have the same velocity relative to some observer, she will observe them both to run at the same speed. That one clock is under greater acceleration than the other has no impact. (Ibix also seems to confirm this for me, thanks).
I don't so much ask why does gravity affect time as why doesn't acceleration? If I understand Einstein's elevator thought experiment, then it seems like it'd be easy to tell, from inside, whether you were on the surface of Earth or accelerating at 1g through space. Only if on Earth would the clock on the ceiling tick more slowly than the one on the floor?
I could be wrong, but my impression is that when you talk about "gravity affecting time", you presume some universal notion of time, absolute time, that exists for gravity to effect. This is not the case in special - or general - relativity. Unfortunately, it seems a bit of a digression to go off and try to explain this point, but it also seems like an obstacle to prevent any further progress without explaiing it.
I shall try another approach, that might be of some help. This is to propose a different experiment, basically a variant of something that has actually been carried out, the "Harvard clock tower" experiment, aka the Pound-Rebka experiment, and compare it to the experiment you suggest.
Basically , a signal emitter is placed at a high altitude, and a receiver is placed at a low altitude. And one looks for a doppler shift of the transmitted signal. One predicts from conservation of energy arguments, and measures experimentally, that the doppler shift exists.
Perhaps it is not at first obvious what this has to do with 'time'. The emitting source can be regarded as being some sort of clock in its own right, and it can be compared locally to some standard clock (currently the standard is a cesium atomic clock), and it can be found that the emitting source keeps the same sort of time as the standard clock.
An identical emitting source can be placed at the receiver's position. This lower emitting source, too, can be syncronized to a standard atomic clock at the same lower altitude location.
But the doppler-shifted signal from the upper clock will not, due to the doppler shift, will not and can not have the same frequency as the non-doppler shifted signal from lower emission source.
So we at least start to glimpse the issue here. The experiment you proposed doesn't show any difference in clock rates. But the Pound-Rebka experiment does. "Clock rates" is an ambiguous term, here, we have several clocks, and just as importantly, we need the details of how we compare these clocks. So we need to be more precise in our language.
So, we need to have the right words to talk concisely about the difference between the two experiments. The one set of experiments shows no difference in 'time', but the other set of experiments does. The right words here turn out to be 'proper time' and 'coordinate time'. There are some other active (and long) threads on this already, it would be off topic to go into all of the details here, I think. The point I want to make is that one can concisely describe the results of the two experiments by saying that in an inertial frame of reference, the ratio of proper time to coordinate time does not depend on acceleration, only on velocity. In a non-inertial frame of reference, though, the ratio of proper time to coordinate time depends on acceleration and position within the frame.
This later observation about non-inertial frames is true both in the case of the non-inertial frame of an accelerating elevator, or in the non-inertial frame that's due to gravity.