What lathe are you using? There should be more than one way to achieve the desired results. I adopted Hardinge's Safe Index programs for use on all our lathes that can use them. The set-up person changes the Z-axis index position based on the longest tool. This is done in a subprogram that stays in the control and is used for every job....and every operation. The post processors are modified to output the safe index programs. Not all of our lathes use these subs. Their post processors are set up with what is hopefully an index position where all tools will clear. Once tools are installed this index position can be changed to a closer position for time savings (or further away if necessary).
I know MasterCam has a home position you can set, but have never used it. No idea how it works. Hopefully it could be output in the NC file. I've been using some of MC for a long time, but it wasn't until 2009 that the company asked me to use MC for all my programs. Before that I hand wrote programs and used MC only to save myself trig work.
I've got to be honest here....I don't understand why someone would run a program without first knowing tools would clear when indexing. How hard is it to change the index position if needed?