No I'm not concerned, as per the op, this is where BMW put the fuel filter for e9x diesels and the Chinese petrol versions.
I've had my 330d e90 for nearly 8 years now & have done about 80k miles in it, I've never damaged the fuel filter, and we have plenty of speed ramps around here! Even if you did somehow bottom it out just where the filter is, the sill's there to protect it. If you crush the sill you'll have bigger problems to worry about!
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Checkout these photos of my 330d's factory fit fuel filter (also notice how different the front subframe is, and the lack of a chassis rail on the inner edge by the transmission tunnel).