For whatever it's worth, I'm leaning toward showing Philippa as the "uncertain" daughter of William (not John) Bonville.
In addition, per Joe Cochoit's reasoning, I'm inclined to add an "uncertain" William Grenville (perhaps husband of a Calmady, per the arms in that stained glass window), as the father of William Grenville, wife of Philippa.
This way, the parents of both William Grenville and wife Philippa will be shown as uncertain, and, if explained well, the whole conundrum will serve as a lesson in the pitfalls and unavoidable uncertainties of medieval genealogy.
Once again, top on my wish list is for someone to examine the original manuscript of the 1620 Grenville visitation, the published version of which showed Grenvilles marrying SISTERS (not daughters) of Theobald Gorges and William Bonville. My sneaking suspicion is that an abbreviation for "daughters" in the original manuscript got misread as an abbreviation for "sisters" in the published version.