Most newer CNC mills (about 25 years?) will allow Z axis movement with cutter compensation still enabled. The reason you usually see cutter compensation disabled in most programs is it allows the tool to be repositioned back to the starting point of repeating a pattern without thought for the tool path between the finish position and the start position. It is not bad practice to leave cutter compensation enabled. It is more difficult on the part of the programmer, which means it usually take more thought energy and time. It is easier to cancel, G40, rapid tool up, rapid back to the starting point of the pattern (a known number instead of calculating a new one), feed back down on Z, the copy the previous cutting pattern, repeating as many times as needed. It is also easier to cancel cutter compensation after each pattern, because forgetting to do so can create other programming problems later in the machining. Finding those errors out later takes more time and effort than just canceling the cutter compensation to begin with.