I had the wallet in the back pocket syndrome. It caused sciatica with me.
I find that many German cars, in manual form, have such offset pedals (try a new A4) that they give me loads of grief (they compromise the design for RHD). It was one of the reason I bought my Accord (perfectly straight wheel and pedal placements). I guess that given the Honda is designed straght off as RHD it makes sense. Volvo have touted straight sitting positions too for many years. One of the reasons, along with great seats, is why they are comfortable.
You might be able to tweak your position in the Beemer however some cars you just never get comfortable. Maybe you need an auto?