I can think of several factors that effect this one of them is the support needed to have a design like the B727 or the L1011 and the DC10 type would be extremly tail heavy. Another reason is the space needed to put the actual engine takes up a lot of room which would mean less room for passengers and cargo. There is a Falcon business jet that has three engines like the B727 but it is a rather large jet almost as big as a CRJ  and in some modles it is bigger than a CRJ so I am not certain what class you would put that into. I know it takes a lot of runway to land and take that plane off in due to the gross weight of the aircraft.
If you ever take a good look at the B727-200 you will notice where the wings are in referance to the engines
Believe it or not there is 1 model of the B727 that before you put fuel on it you must lower the back stairs to prvent the aircraft from tipping backwards. This is a fact not fiction. I was a fueler at KJAX and whish I had a dime for everytime I had to do just that. One of the reasons they reposistioned the wings and added more fuselage up front on the newer models so you would not have to do this. 8)

Another *possibility* is that on smaller jets, the proportional distance of the thrust line above the COG, when the other two engines are "in-line" with the COG, may cause an undesired rotational force...  Note that with the two planes mentioned, MD-11 and DC-10, they also have the two wing mounted engines, plus they're much larger.

Most of the small trijets have the thrust lines parallel to each other.

(Note:  This is pure speculation on my part, as I am not an aeronautical engineer.)