Here is my take on the situation. Tell your engineer that it came from an engineer.
There are two things that are impacted by the manner in which the conduits are laid out in the ground. One is ampacity. The closer the conduits are to each other, the more difficult it becomes for any single conductor to dissipate its heat to the surrounding environment. This issue, in my opinion, is the engineer?s responsibility.
The second consideration is local overheating. It is my opinion that this is the basis for the requirement to ?maintain spacing.? If you wish to discuss the question of how much spacing to maintain, then go to the paragraph above. But let?s consider conduits that are 1 inch apart for 20 feet, then are 5 inches apart for the next 50 feet, then are in physical contact for 10 feet, then are 2 inches apart for the next 30 feet, etc, etc, etc. The ?impedance per foot? of any single conductor passing through one of these conduits will vary from section to section. That is because of the local influence (i.e., inductive and capacitive coupling) of its neighboring conductors. The current flowing in a given conductor will be constant throughout its length. But since impedance varies, the amount of heat (i.e., I2R heating) will vary. It will therefore be possible that the conductor will overheat in one section, even though the total current passing through the conductor is within the ampacity limits of the conductor.
My conclusion is that if you have kept the spacing between conduits ?reasonably? constant throughout the length of the conduits, then it does not matter what the distance is between the conduits. So if I were the engineer of record, I would ask you to describe the method you used to maintain spacing, and would probably have wanted to see the method in place, before the trench was backfilled.