[JMT1985]

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.