It is just an aesthetic choice.
Traditionally in English bespoke shoemaking, black town shoes would have had a 'painted waist', while country-type shoes and 'casuals' (loafers) would have had a natural (stained) sole. But even that is not set in stone: John Lobb has always finished black shoes with an all-black sole, everything else natural.
It might have been EG, who introduced painted waists into their previous top-drawer range (mid - late 80s), to give ready-to-wear shoes that bespoke look. This was subsequently extended to the standard range and other manufacturers (but not all) have followed suit.
If by john Lobb you are referring to JL Paris RTW that is not true. I have plenty of non-black JLP Prestige shoes with 'black sole'.