A structure owner benefits from a higher cost index because their income per job is directly calculated as a portion of the sci. The expense of maintaining the service, however, is a constant, regardless of where the structure is placed.
Contrast the above with Refining. With refining, the tax rate is a flat percentage of the material either input or output (probably output, but which it is doesn’t affect the comparison). This tax rate is easily compared among the available structures for the refining service and a corporation or individual can select one according to their political motives, willingness to travel, or willingness to pay for convenient location. An apples to apples comparison, if you will.
For manufacturing and similar services based on the SCI, there are a number of difficulties. I live in a system at present with an SCI of 0.23%. That means that if I were to set the tax rate at the cap of 50%, I would be able to charge at most 0.125% the value of the industry job, while at the same time players searching for my structure see an astronomical 50% tax rate.
A person living in a system with a theoretical 2.30% SCI could set their tax rate at a mere 5%, which looks far more reasonable, and get the same payout of 0.125%. This comparison is more apples to oranges, in addition to encouraging people to place even more structures in busy systems rather than setting up in un-tapped markets.
The only opposing force encouraging players to spread out is that of competition, but in a busy system that 0.1% tax a structure owner sets can be worth 20 times as much as it would have been elsewhere, lowering the incentive to strike out far from home unless your customers are savvy enough to do their homework to see why your higher taxes are actually a better deal.