One reason for the difference in results might be the context of their construction. Temples in Greece were frequently built upon sites that had been sacred for generations, reaching back into the Bronze Age at places like Thermon, where the later classical temples were built over the remains of Mycenaean era megaron.  There was the matter of historical tradition which meant that temples built in the archaic and classical periods might be built not only according to the cosmology of the time of construction, but also within the restraints of prior religious thought. The temples in Sicily were built in cities that, at the time of building, saw themselves as immigrants in a distant land.  Therefore there was no historical precedent to shape the construction of the temples. They were much more likely to be purely the products of seventh-, sixth- and fifth-century cosmology. The lack of prior foundations gave the Sicilian Greeks more freedom to express current thought in religious practice through their temples.Related: Soil and Greek temples
The self-identification of Sicilian Greeks as Greeks living overseas may have also made adherence to a Greek ideal more of an imperative to reassure both themselves and visitors from the homeland that their location made them no less Greek. It is interesting to note that Greek sanctuaries in Greece could be out in the hinterland tying territory to the city, while Sicilian temples were all built in urban or suburban sites. An ‘astronomical fingerprint’ may, along with other elements such as the architectural form and religious practice, have been part of a drive to prove the Hellenic character of a settlement. Hence, perhaps, the stronger results in Sicily than Greece. This could be testable by comparison with temple alignments in other locations like the Black Sea colonies or Hellenistic Asia. A lack of a similar adherence to astronomical orientation for temples in these regions would be a surprising result given the emphatic nature of the results in Sicily and Greece.
PLoS ONE doi:10.1371/journal.pone.0007903
The Astronomical Orientation of Ancient Greek Temples
Alun M. Salt
Despite its appearing to be a simple question to answer, there has been no consensus as to whether or not the alignments of ancient Greek temples reflect astronomical intentions. Here I present the results of a survey of archaic and classical Greek temples in Sicily and compare them with temples in Greece. Using a binomial test I show strong evidence that there is a preference for solar orientations. I then speculate that differences in alignment patterns between Sicily and Greece reflect differing pressures in the expression of ethnic identity.