Sigil has always updated the modification date on save. The dc:identifier is a unique number that represents that epub and it is autogenerated once and only once. You can think of it like a isbn of a sort. See here for a description of a uuid.
https://en.wikipedia.org/wiki/Univer...que_identifier
Under epub2 just the modification date is set. Under epub3, the modification date and time are set. Under epub3, the spec calls for the combination of uuid (identifier) and modification date/time to always completely identify an epub publication.
I would assume calibre does something similar, as does ibooks author, especially for epub3, as it is spec.