I have done extensive research the past 5 years on the "old" families, primarily for Donnie Blackstone. It was the custom and practice of these old families to "keep" names. The name ALLEN as a middle name for 2 of Joseph Augustus Warren's sons and SEVERAL grandsons is an extraordinary indicator that his wife Abigail was Abigail Allen and that Abigail Allen was the daughter of Abigail ALLYN as the ALLYN changed spelling to ALLIN and ALLEN in later years on Connecticut land and census records.
Abigail Allen Warren may not be the daughter of Job Allyn granted, but I'd go with the fact she was for now until whoever told she wasn't can provide evidence she wasn't.. In the absence of documents in some areas of colonial America, reliance should and must be placed on PROPINQUITY and custom.
You can always write in the bio of Abigail that parentage is probable but speculative and use what I have explained above as reasoning for the connections.