While that is doable, I agree that a 'update to template' button would be very useful. Why make this harder then need be?
*shrug* Why make all your units the same? Certainly the real world doesn't work that way.
I like that after fifteen to twenty years my Militia Battalions have varying numbers of soldiers, and some of my premiere Divisions have extra regiments and/or battalions.
You can do both. The real world does in fact have designated TO&E's for everything. Not everything adheres to those numbers, but there is an intended size and composition for every military formation.
A real life example would be the German military in WW2. There was a set standard for what an Infantry Division should be, operational realities didn't always allow for each and every one to be at that level, but there WAS a set level that they should be at.
Personally, I would just like to see those items side by side. Have what is in the formation on one side, then have the formation template on the right side. You could then have another button called "change template" or something to that effect, that would allow you to change what TO&E you are comparing yourself too. This way, you could upgrade a standard infantry formation to a more modern variant of it.