I suspect the Boro response to you would be to say that they should be awarded the first game as a 3-0 win, thereby winning the tie overall as a 4-2 aggregate..... resulting in us being effectively chucked out. And that would set a 3-0 precedent for future ordinary league games.
However that would also be a potential legal minefield because if we'd known before the second leg that we were 3-0 down, we'd have played differently in the second, taking risks and going hell for leather to score 4. Awarding it as a 3-0 win *after* the second leg disadvantages us unreasonaby. So we could use that in an appeal.
All round the EFL have really cocked things up by setting a rule without setting a standard punishment for breaking it.