I use the Dot 5 fluid in several vehicles and if simply changing the fluid over from Dot 3 or 4 to 5, then I use the alcohol to thoroughly flush the lines.  In doing this, the master cylinder and wheel cylinders are in a state of disassembly or disconnected from the system so only the lines are getting cleaned with the alcohol at that point.  The master cylinder and wheel cylinders are completely disassembled and cleaned by themselves when doing the brake fluid changeover.  Be sure to air blow the lines thoroughly when through and allow enough drying time before reassembling the system.