[Stooky Bill]

Quite simply, M&S is a commercial business, and the BBC wouldn’t want to give undue prominence to them, so that’s why the M&S logo is being covered up.

On a side note, the "undue prominence" rule at the BBC seems to be enforced only when the BBC feel like it - just look at many shows past and present, and real life commercial products are always seen fully on screen. Most famously Only Fools and Horses seemed to show nearly every household product that was on sale in the 80s and 90s, from the Daily Mirror, to Asda shopping bags, to Kellogs Cornflakes etc, with none of those products turned away from the camera. 

In Mrs Brown's Boys, Brennans Bread is there in her kitchen every edition, a bread which is real and is sold in Ireland today.

That's because undue prominence is more an issue on commercial TV because that has paid adverts. For example having a prominent shot of a box of Kelloggs cereal when Weetabix are advertising in the break is unfair to Weetabix. 

It was traditionally not a problem on the BBC, that was until things like UKTV came along. There was an example I heard in a training session once about an episode of Birds of a Feather (shows how long ago this was!) where they walked in and put some Tesco Bags front of shot on the kitchen counter. It was fine on BBC1, but caused issues on their other channels like Prime and UK Gold 

Of course the BBC is a lot more careful brand names generally now, but that's more a sensitivity due to reputation than an actual rule