The difference is in how the track is built versus how it is driven. The track itself must remain the same between versions aside from the given exceptions, but the route taken in each version has no restrictions except for those given. Let me steal Shadokk's lovely picture to help illustrate this more clearly...
Each line represents one version of the course, with the only differences between the versions here being the start/end positions and the CP's direction. Were any other block placed differently (for example, moving the freewheel block to the other side of the CP for one version), then the maps would not be following the rules anymore and would risk disqualification.
Notice, however, that the two routes do not follow the same path. Route A cuts a corner Route B has to take, while Route B takes a higher road that Route A simply cannot reach. Both routes still have to pass the CP (and if there were multiple CPs present, the order each route took would matter) and each route must still end where the other starts, but Route B doesn't have to be a simple reversal of Route A.
(I'll go ahead and edit "roads" to "routes" in my previous post to help make this more clear)