As established at the tournament section of the game manual,
Is there any exception for this rule?
No. Is there something your getting at?
I recently came out from an event in where for the elimination round, was used the format of the first alliance to win two matches advances, instead of the single elimination format.
Stolen from vex discord:
Yeah, there are no exceptions, and it seems they just play a rematch if there is a tie.
This tied-match exception is a real exception and is defined in the game manual.
Most people just don’t think about it because it’s such a rare scenario to even have a single tie, let alone 3 in a row.
If the EP changed elimination to best of three, where the alliance must win two rounds before advancing, then that should not be considered qualifying. That point was brought up in the EP Q&A. So, if this is the scenario you are wondering about, I would contact the RECF Regional Support manager and ask if the tournament is considered qualifying since it did not meet the criteria for a qualifying event, and if it is allocating spots, ask what rationale was used.
There’s also the case where the EP might put in a match as a tie in TM to force another round, and then just manually record who win and that’s the final one they record.
Or they could just only record the winning match if they did this unofficial best 2 out of 3.
I don’t get all that nonsense. Just follow the rules, have fun and go home.
In some cases those things are contradictory 
NO THE RULES ARE SO FUN SON!!!
Sadly the GDC seems to agree with you.
Here is the link to those matches (I have started it at the time when the first match started). They were insanely fun to watch.
Thanks, @dbenderpt for posting the video. It was great to watch it live. It is cool to watch the replay. I will admit to having flashbacks to Skyrise.