Did they do an update since Friday? If not, while you are correct that it cages the pod, you dont undesignate between stations and stepping has no negative impact. (At least not as of 2 days ago, I cant get on to verify myself, but you havent said anything that is "news" to me, it tracks as I expect.) You only undesignate after you have programmed the very last jdam, that way you dont write over a previous coordinate.
The only hickup "might" be if you stepped to a station that was PP. Just set them all to TOO first.
Once programmed and undesignated, pull up your HSI and it will give you the direction to the target coords of the current selected programmed target.
Follow as I lined out above. Progress linear, dont revisit stations until you undesignate. You will find that each TOO retained the programmed coords. I've done this over a dozen times in the last week eith 8 targets. Again, unless they updated since Friday. Also, speaking to Open Beta. Im new here, so that may be pertinent if its not "standard."