I have a site collection with 5 child sites all using the publishing
template.

At the root site collection, I create a site column called "Display
Location" set it to a choice, and give it 2 options "A" and "B". I then go
to the content types and under publishing layouts > article pages, i add the
new column I created from existing site columns, and click the yes button
"update all content types inheriting from this type"

It propagates this change to all the child sites.

So I go to the page library on a child site, and choose an article that has
been created already, and modify its properties to be Display Location of A.
Check it in for publishing.

I put a CQWP on the child site and am able to see the article when filtering
for Display Location is equal to A.

The problem comes when I try to filter on the root level site collection. If
I use the same webpart settings above on the root level, nothing shows up,
even while making sure the webpart's scope is over the entire site
collection.
So this is where I am at now, and the more poking around I do, the more I
feel it might have to do with the way I provisioned the columns. Is there a
proper way to do it?

If you have any recommendations regarding this issue, I really appreciate
any advice at this point.