The Pennsylvania Supreme Court, however, ruled that they could come in three days late -- due to the issues with Coronavirus and the Postal Service delays, and that ruling has been appealed by Republicans to the US Supreme Court. So, now the Supreme Court will rule the final "verdict" on the late ballots.
As you point out, the SCOTUS would likely not want to "disenfranchise" voters. At the same time, since there aren't enough ballots to change the election and because they don't want courts overruling the legislature, they now will likely order the ballots thrown out. The voters of these ballots won't be disenfranchised since it can't affect the outcome, just the vote totals.
