As for atomic engines being placed on struts, I figure that is due to the ease of jettisoning the cores in the case of a meltdown.  And the reason for planets not wanting them used would likely be simply because of the danger of a mishap during their use within that planet's atmosphere.  No planetary government wants a starship to jettison their nuclear cores down upon that government's planet after-all.  The nuclear output we can create today far exceeds that of the atomic bombs of WWII.  Imagine what an atomic engine of the far future, capable of flinging a large starship into the Void would do to a planet if it went.  Thus, most populated planets have laws restricting the use of atomic engines within their atmosphere.  And of course, the struts would need to be much stronger then those used for ion pods for reasons described in the first paragraph, as atomic engines, much like chemical engines, working in an atmosphere with friction and gravity strained the struts due to sudden unequal momentums on the pods and hull and ultimately tore themselves from the rest of the ship as they fired off .  In the end, all things considered, it's both safer and cheaper--at least construction-wise) to go with chemical engines when approaching a planet with gravity or a heavy atmosphere. 

 

Sure, I see no reason an ion drive could not go into the stern of the hull itself, so long as the financiers and crew were okay with the fact that they would be building a larger craft that would act, space-wise, as a smaller craft.  It's a very inefficient use of space though.  Ion engines would require much more space then chemical engines.  You are squeezing that whole external pod inside the ship after-all, and still having to make room for the chemical engines and fuel tanks.  Remember, ion engines don't work well in gravity situations, so you still need something with heavy "thrust".  

The ship would most likely need to be a big ship for this kind of placement to work. Perhaps something like the Battlestar Galactica, with it's big oversized stern, allowing for both kinds of drives in the same area, thus freeing external pods for either atomic drives or other things like hanger bays in the case of the Galactica.  And like the Galactica, those are the kind of struts, "big and reinforced", I see you needing for atomic drives that functioned inside a gravity pocket.  

Now obviously, this is just my interpretation based on physics, the rules do not stipulate this and there is nothing to say that in the future, ion drives have not been made smaller and perhaps even with more thrust.  Though I don't see how the laws of momentum would change much.  Still, thats the fun of sci-fi