can't you just cut out some space for the rail on the all-weather rubber liner? if you do it neatly it shouldn't look bad! (but if you're looking for a waterproof solution than this wouldn't work for you)

i just want a rubber mat to protect the carpeting... so cutting out for the rail doesn't sound bad...

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2012 X5 50i M-Sport
2014 X3 35i M-Sport