it is not certain given that the results this year can change as we have already seen, and it is no coincidence if teams like these manage to score and move forward in the competition, it is not easy but not impossible so everything is up to them to commit and show that even small things can hurt
A mediocre club like them often makes the big teams unprepared and brings surprises and different colors, as achieved by Lille when they beat Real Madrid they played quite well in any aspect not being careless in closing the space is a good thing they showed. So I think the same as you said that these small teams usually make the standings more chaotic but in the end they will also come out maybe in this round they can be a little bit of a tunnel but walking again I think the small teams are gone
It is somehoe complicated for most clubs, if not all of them in UCL due to the new format, but that will only be a problem to these clubs in the group stage, after this stage the qualifers will be able to use whatever strategy they plan using to win their opponents in the round of 16 and so on, because the rest match will be played home and away. This is why you are seeing a big club been defeated by a mediocre club, and you should expect such in group stage. Girona will not survive the group stage, and if they do, round of 16 will be the end for them.