I don't have access to Byrhtferth in English either but I did track down the passage from Bede:
"The smallest time of all, and one which cannot be divided by any reckoning, they call by the Greek word ‘‘atom’’, that is, ‘‘indivisible’’ or ‘‘that which cannot be cut’’. Because of its tiny size, it is more readily apparent to grammarians than to computists, for when they divide a verse into words, words into feet, feet into syllables, and syllables into quantities [tempora], and give double quantity to the long [foot] and single to the short, they are pleased to call this an atomus, as they had nothing more beyond this which they could divide.
In exploring the nativities of men, astrologers likewise claim to arrive at the atom when they divide the zodiacal circle into 12 signs, each sign into 30 partes, each pars into 12 puncti, each punctus into 40 momenta, and each momentum into 60 ostenta...
...The Apostle uses the term for this kind of time in a better sense, to suggest the swiftness of the Resurrection, stating, We shall all rise, but we shall not all be changed, in a moment, in the twinkling of an eye, at the last trumpet. This deserves our attention, because although computists make a strict distinction [between these terms], many writers indiscriminately call that tiniest interval of time in which the lids of our eyes move when a blow is launched [against them], and which cannot be divided or distributed, either a momentum, a punctus or an atom"
The word translated as "moment" in the passage Bede quotes (1 Corinthians 51-52) is "atomō" in the Greek but was "momento" in the Vulgate which Bede probably was himself using, which is where the confusion in terms he complains about probably originates.
Bede definitely uses "atom" as a more general philosophical idea of an indivisible unit (for any given thing which can be measured) rather than specifically as a practical unit of time. I'm not sure where the value listed for an atom of time in later works comes from, possibly from trying to put a number to the reaction time of a flinch as Bede suggests (any such number would be a complete guess of course, impossible to measure at the time).