The “Ignore Size” option can be used to ignore the size of files in the directory comparison.
This also switches the content comparison off. Diffoniq reaches a file’s contents through its size: only pairs of equal size are worth hashing, and that check is where the content verification happens. With the size out of the picture there is nothing left to trigger it, so a pair counts as equal as soon as the attributes still being compared (date, time, name) match — whatever the files contain.
That is useful when you deliberately want to compare by timestamp alone, for example against a backup that rewrote every file. If you want to know whether the contents match, leave the size switched on.