Senior SRE Paul Shuvashish first noticed that these emails weren’t failing DKIM but SPF. [...] This pointed out a flaw in our application-level analysis system: we were assimilating DMARC errors – which can be either because of SPF or DKIM – to DKIM errors. So while the app was doing the right thing nevertheless – marking the email as spam – the insight it was collecting internally was misleading.

I don't agree with 'the app was doing the right thing' here: for DMARC alignment (a DMARC pass) you need SPF or DKIM alignment. One of the two is enough.

So an email from a domain with DMARC enabled that passes DKIM, but fails SPF should pass. The application should not have rejected the email based on SPF, when it was actually DKIM aligned.