William Penn wrote three different frames of government documents. All three are different, so therefore which one do we go by? How do we read them? And which one is the final document that PA uses?
I think this question is entirely answered by Wikipedia
The Frame of 1701 remained the governing constitutional document in Pennsylvania in the following seventy-five years until the Revolution of 1776. Wikipedia
Given that the source of authority for the Frame of 1701 was the crown, (see below), in 1776, created a new governing document.
WHEREAS King CHARLES the Second, by His Letters Patents, under the Great Seal of England, bearing Date the Fourth Day of March in the Year One Thousand Six Hundred and Eighty-one, was graciously pleased to give and grant unto me, and my Heirs and Assigns for ever, this Province of Pennsilvania, with divers great Powers and Jurisdictions for the well Government thereof. Frame of 1701
The following is included because comments are ephemeral and I don't want to lose valuable information contributed by others; neither do I want to claim their contributions as my own. Please update the answer rather than commenting.
@LangLangC provides another source with similar information
To resolve this dispute, in 1701 Penn issued the "Charter of Privileges," which granted the General Assembly the right to initiate legislation, and therefore, took away legislative powers from the Council. The Charter of Privileges remained in effect until Pennsylvania declared independence in 1776 during the American Revolution.
None of these charters are used for governance today. In 1776 Pennsylvania chose to create a new governing document. Note that all legal documents may be cited in later cases, but that is not "used" in the sense that I interpret OP's question.
Quote from @LangLangC,
Concerning "uses", since 1776 the Pennsylvania constitution is in use, no the Frame of Government. Perhaps the Wikipedia legacy part (eg Bader-Ginsburg quoting from frame) was source of confusion for OP? But that just means the Frame 'is still used today' - as an inspiration, or point of orientation - not as a legal basis for anything. Also noteworthy, the possibility of "amendments" meant the Frame was intended to be adapted "as needed", which it no longer was in 1776.
@Cmonsour points out that some states retained their colonial charters as their state constitutions until several decades after independence, to show that rewriting the state constitution was not absolutely necessitated by independence.