We agonized about this a lot when implementing arbitrary deadlines. See section 4 + the appendix of the arbitrary deadlines spec.
Short answer is that the data has the true timestamps but we do treat the deadline as the day boundary for purposes of graphing and displaying. It became a worse-is-better vs the-right-thing debate and I predict @mary will be horrified that we rejected “the right thing” but, well, read about the worse-is-better philosophy before yelling at us too much… (:
PS: Speaking of being horrified, I clicked like on @philip’s reply here since it’s contributing lots to the discussion, as always, but let me disavow the craziness of mirrored goals as a solution to this! (: My first reaction to your “export calendar-day-datapoints” feature was that it’s overkill but if it takes something like that to avoid the contortions you’re going through then it may be the lesser evil…