You don't have to use the IPE software to program the chip.

MPLABX (and the older MPLAB) has command-line drivers for each of the programmers (PK3, ICD3, etc).
Using these you can add the Pickit3 as a programmer to the MicrocodeStudio IDE and then you can program the chips directly from there.

That way you don't need a bootloader at all.