However, it must be noted that plain and simple this conversation dictates on common sense (oh no did I just use that term on a VATSIM discussion board ). What time of day is it, What day of the week is it. How busy is the NAS. Are there any events taking place nearby (especially at the destination airport or other airports along their route). What airport are they going to. Is that a large hub and busy airport. Is it a satellite field of a large hub and busy airport. These and more are all factors to consider when answering this question.
For example when working ZID I will give "direct to" clearances all the time. Probably 10 times more than when controlling ZTL. It all just came down to how the airspace was designed and how tightly compact that section airspace is they are flying through. Also that ZID saw a lot more en route traffic where ZTL is heavily populated with arrivals and departures.
Thanks for locating that section. I looked for it before I posted the above, but missed it. Another piece of it is the note at the bottom of the section. I like your interpretation.
[!--quoteo--][div class=\\\'quotetop\\\']QUOTE [/div][div class=\\\'quotemain\\\'][!--quotec--]NOTE−
Nothing in this paragraph must preclude a controller from
issuing a routing clearance that conforms to a letter of
agreement or standard operating procedure within their
own facility or between facilities, is required to maintain
separation or comply with traffic flow management
initiatives.[/quote]