What do you mean when you say 'Through" the top? If its along the top rails, thats fine, loads of people do it, I'm doing it local to the bell housing cos of space issues around the clutch cable/fork bit. If your talking about inside the rails..... thats a fail, cos you ain't supposed to touch the chassis.
Also there won't be a problem with the design, after all look how many cars are on the road. If you have a hole in your system and its leaking, where you caliper is in relation to the master cyclinder, is going to be awfully irrelevant as your car launches its self into a field.
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