As I pointed out the distance savings LA-SF is only 5%. The Central Valley is a vast area, and Interstate highways all over the country were routed thru farmlands. As far as routing, I can see on Google Maps Satellite View that in few places the aqueduct and highway are in immediate proximity, in most places they are several miles or more apart.
One article did point out that there were many places where the highway design and construction needed large amounts of borrow excavation material (that obtained outside of the highway's right-of-way) to sufficiently raise the highway grade above flat terrain so that the highway will drain properly, and that material could be obtained from the canal construction several miles away.
Borrow excavation typically costs twice as much per cubic yard as does regular excavation (that moved within the highway's right-of-way), because the obtaining of borrow pits usually have to be negotiated between the contractor and a private landowner. If the borrow material is in another public works project a few miles away that needs to have large amounts of material removed and disposed of somewhere else, that would considerably reduce the cost of it, both for the highway project and for the canal project.
That's a more than reasonable assumption; and almost certainly one that was utilized back in the early '60's during construction of the initial phases of both parallel projects. In the process of skirting the fall line of the hills to the west, there was a lot of "cut and fill" across the various drainages on I-5 as well as I-580, and much of the material removed from the cuts was deemed substandard for fill purposes (more rubble than dirt, according to my cousin, who was on the Division inspection team for that phase of the Westside project); the material removed from the somewhat downslope location of the aqueduct canal was deemed better suited for that usage (would pack down better).
Not sure how 'rubble' is defined there, but rocks and stones and pebbles are not in and of themselves a problem, but there are certain types of soil that make a solid highway subgrade, and there are other soils that do not have the needed load bearing capacity. Most any highway right-of-way corridor will have both types and it is the job of the designers and construction engineers to ensure that only the right types are utilized.
Highly organic soils and topsoil are unsuitable and are removed and disposed of or saved for other uses where topsoil is needed.
Here is a good overview --
"Many different types of soils may be suitable for use in the construction of an embankment or fill, ranging from granular soils (sand and gravel), which are highly desirable, to the more finely sized soils (silt and clay), which are usually somewhat less desirable. Certain types of soils (such as saturated clays and highly organic soils) are considered unsuitable for use as materials in embankment or fill construction. Regardless of the type(s) of soil(s) used to construct embankments or fills, the material should be well graded, capable of being well compacted, be within a proper range of moisture to optimize compaction, and be free of unsuitable or deleterious materials, such as tree roots, branches, stumps, sludge, metal, or trash."
https://www.fhwa.dot.gov/publications/research/infrastructure/structures/97148/app4.cfm....
In cut sections it is still necessary to have enough depth of suitable material, and in some areas undercut excavation is needed to remove unsuitable material, which is then backfilled with material that has been deemed suitable.
