I would guess you will get away with the modifications you mention until you need an insurance claim.
Then if the vehicle is inspected it wont be an MOT chappy but an insurance assessor who may notice the differences between a rebody and a new chassis component. After all they dont want to pay out and any excuse will mean its null and void.
Its not an issue for me I bought the Sammio as I like the look and the simple home mechanic set up and I am happy to keep it fairly stock, I think that is the whole ethos behind it.
I think you will also find the bodies are fixed/ glassed prior to the inspection and not loosely fitted, I may be wrong as I am not there yet.