The issue is the powers to agree a budget with the club under e.15 are in addition to the requirement to keep within the financial limits under the earlier part of Part E.
Notwithstanding the fact that a budget may be required, the PL still has the power W to sanction any breach of accounting rules by way of the sanctions stated under W.
The ability for the Prem to appoint a commission is separate to e.15 which is why Leeds and Burnley are asking for one.
Where 15.E is relevant is that it may show the Prem have already considered whether or not to puruse further sanctions, having acquired the necessary further information under 15.E ( and agreed a budget in lieu if this has happnened), therefore an Abitrator would be likely to find the matter has been properly repsonded to in accordance with the contract.
The fact that E.15 has been used as such does not exclude further action under W however.
No it does not.
And we do not know, formally whether than has been invoked. Theres nothing official to say it has, though it looks like both parties have unofficially decided to follow its guidance.
In that circumstance, or indeed if it were deemed as the punishment for an offence (which crucially to date has not occurred) I would say it would be unusual you would do punishment E, and then punishment W, especially if the club was showing willing to follow E, which given what has happened certainly seems to be the case.
Why have those rules in, if you would override them?
The other critical point, is to date, no breach has happened. So E, W or any other permutations have no relevance until that is established. Everton have shown losses under the permitted level, have had those accounts signed off as legitimate, and we have been told the PL have also signed them off as acceptable, having been given the full working of the uncrystalised losses.
If the PL wanted to punish the club in this season, it would need to have raised that the breaches have been failed within this season. There are 24 hours to go to do that. After that, really any punitive punishment would be next season (of which there is a range of options, with points deductions being at the sharp end).
I should add, I am not sure what would prompt such a U turn from the PL, and I am doubtful it would hold up in a court. Businesses are allowed to do write downs. That is perfectly normal practice, especially in the midst of a global pandemic.