When designing the outlay of the main category index pages within the overall page structure there are two basic options:

a) one within each folder
(Apache seems to want to see a dedicated index page that has an extension such as... page.htm/index.htm
With the added index.htm tag (or php variation, etc)

a.1) OR, putting a page that functions as an index page within the folder that has the same basic page extension like all the rest.

b) OR one outside the folder structure, in the main site root.

Does it really matter to Google and the others which is used as far as indexing is concerned? Do they give weight or preference to any including if a single anypage.htm is used that functions as an index within a folder?

It's not always practical with larger sites to place single index pages within the folders as many topics cross paths while others are more consistently-themed by nature.