Hi Coinmeister - and welcome to the forum.
It's a good question. As you already know, at the moment, Alliance & Leicester operate under a separate FSA authoristation to other UK based brands in the Santander group which includes Abbey, ASDA, Bradford & Bingley and Cahoot - so £50k with A&L and £50k in one of the latter are both - currently - separately protected. I believe this will continue to be the case for any existing savers, but this will change for new savers once the 'merger' takes place.
I'm just in the process of checking this with Santander, but as I understand it, once the brands all come together under the Santander umbrella, there will only be one FSA authorisation - so if you had £50k with A&L and £50k with, for example, Abbey, you only have protection up to £50k under the Financial Services Compensation Scheme, unless it's a joint account in which case you have protection up to £100k.