You may see the pll_cal_busy signal of the Intel® Arria® 10 ATX PLL assert when the internal configuration bus is returned to the PreSICE even though no ATX PLL calibration is requested. This is a known issue with the Intel® Arria® 10 PreSICE.
If ATX PLL calibration is not required, write the value of 2'b00 to offset address 0x100[1:0] before the internal configuration bus is returned to the PreSICE.
This has already been fixed in Intel® Quartus® Prime Pro Edition Software 17.0.