You bring up some excellent point X not the least being the one above. I recall when I was in the service I was assigned to relatively small units. I was blessed that I had some excellent chaplins but, as you stated, many of them served multiple denominations. In fact our group were so small that often we attended different worship services just to support the chaplins. There would be a certain irony if an atheist had to perform a baptism.
What is most interesting about your point and this article is that the atheists don't seem to have a clue as to how the military works or what would be required of them. If they did, they certainly wouldn't make this proposal.
These atheists certainly don't have a clue. Others have been serving in the military for years with no problems.