The pivot command currently (v6.2.1) support the median but not other percentiles.
However, if you simply want to have the reports using datamodel acceleration rather than the drag and drop features of the pivot UI the you could use tstats. The tstats command will use the tsidx files of your accellerated datamodel and you can use perc, exactperc and upperperc.
| tstats p25(Duration) AS p25 p50(Duration) AS p50 p75(Duration) AS p75 from datamodel=SomeDataModel
BTW, for something more complex you might create a pivot via the UI, run it and inspect the job which gives you the tstats command which you can then modify / develop further.