The preposition by in this context means
not later than: be back by ten o'clock
The original sentence means
You must have it in by a given amount of time.
The phrase have [something] in by is common and often followed by a particular deadline.
Have it in by 3PM.
Have it in by the end of the week.
Because the definition you read was not setting a particular deadline, but referring to a more general given amount of time, using the phrase by a given amount of time would sound a bit awkward to most native speakers. By would more often be used for a fixed deadline, not a time span. Most native speakers would more likely say
It means that there is a given amount of time to get it in
It must be in within a given amount of time [which means it must be submitted within a given amount of time]