Usually differences in prices are explained by fare class inventory or "bucket" availability. The most attractive schedules/routings are more likely to sell out first for the cheaper (and eventually more expensive) fares. You can see permitted routings in the fare rules (if you can actually view them on delta.dumb, as should always be possible).

Having said this there can be systematic differences based on how competitive a routing is. For instance, if more carriers fly TPAC/TATL from LAX than SAN, then the LAX fares can be expected to be lower on average. One sometimes sees differences that are apparently derived from differences in landing fees and other costs of operations at various airports.

Purchasing separate tickets on different carriers is very risky unless you allow lots and lots of time--ideally overnight on the outbound--to connect. Then the cost of the hotel, meals during transit, additional time away from work, etc. can be greater than the potential cost savings.