There do seem to be some oddities in the records that you have cited. Boyd's contains huge amounts of information, but it is a secondary source. Looking at the list of children and the baptisms dates, it is obvious that whoever wrote out that list did not question the dates.
Assuming the children were baptised within a few weeks of their birth, it is not possible for there to be two children born in late 1658 to the same parents.
While Boyd specifically notes that there are some children not mentioned in Richard's will, it is still possible that they did not survive: the burial has simply been lost in the records. (Don't forget, the Great Fire of London wreaked havoc on 87 churches in 1666.) That said, I suspect that Boyd got some of his information from a secondary source: the transcription of the parish register published by the Harleian Society (published 1877), which has the following entry on 10 December 1658:
Paul late sonn of Richard Blackburne, draper, borne same day
Looking at the original register entry, it has clearly been mistranscribed in that printed transcription. The rather elaborate 'L' has been read as a P and the last four letters have been read as a separate word - 'late' So this is why transcriptions are not necessarily the best source and the original should be checked where possible.
One a general note: the 1650s was the time of the Commonwealth and many parish registers are deficient or messy. While it may be true that the complete extant register has been digitised, it does not necessarily follow that every event was faithfully recorded in the register. I was looking at a parish register earlier where it is obvious that various slips of parchment/paper have been stuck on new(er) backing sheets, presumably because they had fallen out or were not bound in properly. Some may well have been missed.
Nell
