This is fairly simple, and is entirely different to the "last case" as posted above, in relation to floors.
This covenant is a clear "you, the lessee, shall not" but you have.
There is a strong argument that if the landlord was aware of the works and you have paid the ground rent and or service charge that they have waived the ability to forfeit this breach. If the landlord gave consent for the works then that too should be sufficient.
The absence of building regulations also creates a doubt in their mind that a defect might be present which might re open the whole matter, with the landlord requiring rectification, re instatement, and given the clear NO in the lease a premium.. More importantly as the lease is clear
A buyer would understnadalbly be concerned but knows that
1: this would have to bes estalbished in court at cost or
2: A far cheaper DoV.
As this would have been required at the time( in order to sell at a future date) you had to get one sooner or alter.
Frankly I would not agree to a with consent variation of the above, it should be limited to internal planning and non load bearing walls, the remainder should not be interfered with save for repair.
Based on the information posted, I offer my thoughts.Any action you then take is your liability. While commending individual effort, there is no substitute for a thorough review of documents and facts by paid for professional advisers