It is true that Google (and other search engines) does not count some very common terms (like ‘the,’ ‘a,’ and ‘for,’) for the sake of efficiency; while search engines index entire copy of a page including stop words but they are said to be not counted (to be ignored) to determine how relevant a page is to a specific search query same thing is true for the other way around; meaning that stop words in search queries are usually not counted (they are ignored) unless omitting a stop word makes a big difference in the information the user is looking for; in this case they won’t be ignored.

One example that omitting a stop word would make a big difference in the returned search results can be observed by Googling these two queries “the who” and “who”. If you search these two on Google you will see that “the who” returns results related to an “English rock band” and “who” returns results related to “Word Health Organization”

On the other hand, It seems that having or not having stop words in a text link do not make a major difference in the final rankings of a website for one specific targeted key phrase. For example if you are targeting “orthodontist in Miami, FL”, you can both link back to your site using “Orthodontist Miami” or “Orthodontist in Miami” as the text link (anchor text).

But in your link building efforts you must use both versions (with and without the stop words) and even you have to use other versions of the same key phrase such as reversed version (Miami Orthodontist) or plural version (Miami Orthodontists) to look natural to Google in order to avoid being penalized for one specific key phrase.

If you have a set of keywords that you want to write an article based on, as far as content developers are concerned, if a stop word in one of your key phrase get in the way of writing naturally and omitting it won’t make a big difference in the returned search results I would advise to omit it.