This is correct because your train emitting from the portal is "blind". There are no driver or commands assigned to the consist until the complete consist has emerged from the portal and the consists will speed along at 40 mph blindly blowing through any signals and switches without any regard to their aspects or routing.
My solution is to place a blank baseboard or two and place the portals as far away as possible to allow the consists to emerge completely and come alive before entering into the route proper.
