Changes to the original planning permission during construction

the only answer to this is to talk to the architect/engineer who will be signing off on the completed build, if they are very minor differences then they may be happy that what is built is in substantial compliance with the planning permission.

Changing the position and size of windows and adding a porch are hardly minor alterations?

tbh i didnt even look at what the OP was talking about specifically since my advice would be the same unless they were talking about something that would be blatantly not allowed under substantial compliance

windows could be minor depending on how different they are to what was shown originally and i would say what exactly constitutes 'minor' would vary from person to person. i worked under people who would be happy enough to sign off once it looked something like the planning drawings (hyperbole of course) whereas most other professionals likely wouldnt agree

This is the correct answer. Make it official, it's not a new application, even if refused, the original is intact.

Back up option would be any works post completion as exempt works (may only partially apply).

Architect/Engineers opinion has no actualy bearing on planning permission. Whether they are willing to sign off (or not) does not make it acceptable (or not). If you got stuck with future costs, you could use that opinion to claim from the architect, but that's a separate matter entirely. Or if you need that peice of paper for the bank/buyer - again a separate issue.

Finding somebody to sign off it usually easy. The lower the fee, the less detailed look they'll take. Could probably even get somebody to sign off from a photo without a site visit. But as above, it actually changes nothing regarding grant of permission