The situation leaves a shroud of uncertainty over the play-offs before the second leg. And it will continue to cast a cloud if Southampton get to the final.
The independent disciplinary commission has all powers open to it - from just issuing a fine, to a points deduction to even removing Southampton from the play-offs.
For this reason the EFL - which does not decide the punishment itself - has asked for an expedited hearing, with the play-off final scheduled for the day after the 14 days expire.
With even the mere possibility that Saints could be thrown out and Boro reinstated, the matter needs to be resolved as soon as possible - especially as there would be the right of appeal.
Seven years ago, Leeds United were fined £200,000 by the EFL for watching opponents train before matches.
A member of Leeds' staff was found acting suspiciously outside Derby's training ground on 10 January 2019, before a fixture between the two sides.
But this is not a direct comparison.
At the time, there was no rule which covered spying. Leeds were only charged with failing to act towards another team with "good faith".
Following the Leeds case, the EFL introduced rule 127, which specifically forbids any attempt to watch your opponents in training in the days leading up the game.
As Southampton have been charged with both offences, it may well be that a fine is not enough.
That the Saints spied on a rival before such a crucial match, whereas Leeds watched a league game in the middle of the season, could be seen as an aggravating factor.
Leeds boss Marcelo Bielsa, though, did say he had sent a member of staff to watch the training sessions of every team his side had faced in the 2018-19 season.
Much may depend on the full details of the case, how much senior members of the coaching staff knew and what was recorded or transmitted. This would only be mitigation rather than any kind of defence, as the 'spy' would still be representing the club.
A points deduction could be imposed, though Boro will question if that is sufficient should Saints get promoted to the Premier League.
The EFL cannot impose sanction a sanction upon a club in the Premier League, but it can recommend one.
It would be then be up to the Premier League board to decide if the deduction should take effect in the 2026-27 campaign.
Perhaps football's most high-profile case of spying came at the 2024 Olympics women's tournament in Paris.
Fifa deducted six points from Canada after they were found to have spied on New Zealand using a drone.
World football's governing body also banned three members of Canada's staff, including the head coach, from all football for a year.
Southampton may have asked for more time, but that is something the EFL does not really have.

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