One interpretation that I always have in mind is that system ships and warp capable ships are constructed to very different standards, because they must be used in very different environments.
While the vacuum of deep space is an extremely hazardous environment, it is nothing compared to the nightmare realm of the warp. Although the Gellar field should be able to protect the ship from the majority of daemonic interference, a warp capable vessel must still be constructed to such an astonishingly high standard that it can survive just about anything, even if the field fails. All we see in Battlefleet Koronus about the construction of warp-capable vessels hints at the degree of over-engineering inherent in their design. Imperial vessels that are kilometres long have been recorded as landing on planets, or crashing and being recovered after spending centuries buried underground.
while you could theoretically bolt a warp engine to a system ship, I feel this is a bit like attaching an outboard motor to a child's toy dinghy. I see the vacuum of deep space as travel on a pond, whereas warp travel is the open ocean.
so while a Bastion class system ship might be well armoured and survivable in combat, it lacks the structural integrity inherent in the designs of true warp capable ships.
That's a very personal and subjective view, though! :-)