Top level category
First, thanks a lot for all the maintenance work you have been doing; it's good stuff.
You are correct in observing that the Category:MainIndex will remain un-categorized, but such is the fate of the topmost category! It's the same on Wikipedia, where Category:Contents belongs to no category.
The idea here is to prevent category-linkage loops, to avoid confusing the bots. These would normally process categories recursively. If you've done any recursive programming, you can see how a closed loop could lead to infinite recursion.
If you edit Documentation/How_Tos you will see that most of the HowTo entries are gathered automatically by the <DPL> feature, which lists all the pages in a category. However, the Templates HowTos are not automated, and they should be. This means going to each entry, changing the category from doc/howto to doc/howto/templates, then creating that category (and categorizing it in doc/howto). Then add the automatic stuff to use the new category. There are some (at least one) pages in Category:Templates that should be included, too.