DMcG:
You may be reading something into that article which isn't there, or I may be missing something in it.
It does not state anywhere that it is in relation to the 12 million mentioned in the earlier quote.
In fact, the earlier quote makes clear: But the disclosure, at a time when Electoral Commission investigations into leave campaign financing are continuing, will raise serious concerns about the ease with which laws restricting campaign spending can potentially be circumvented
So is the fine mentioned today in relation to the 12 million? or to the investigations in general?

The Commission has already been shown as ready to investigate any complaints about LeaveEU spending, while not investigating spending by the Remain team. And in response to the fine (from today's article):
Leave.EU co-founder Arron Banks called it a "politically motivated attack".
Responding to the Electoral Commission's findings, he said: "What a shambles, we will see them in court."

I think we should wait to see exactly how this plays out before anyone starts crowing.