Yes, combining resistor values using arrays is good idea. I have used that approach in some other projects. I especially like to use resistor arrays as feedback resistors for opamps, when minimal temperature drift is needed. Many resistor arrays have a specification for matching of temperature coefficient, so they cancel out nicely. This is cheaper than buying separate resistors with small PPM spec.
Actually, my original target for reducing PICkit2 BOM was to allow easy integration to PCBA test systems. So I wanted to use parts which could be already on the tester BOM.
Using crystal-less USB on PIC18F25K50 is not flaky. It has ACT (active clock tuning) which can sync to USB host clock. I have used it in several projects, including commercial ones, and it has been working without problems.