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As an eea national your son would only qualify for permanent resident wants he has lived in United Kingdom for 5 years exercising his treaty rights.
This means that he will be eligible to apply for permanent residence after 5 years studying in the United Kingdom provided that he has spent most of his time here.
If he commenced his studies in September last year and will return in September this year then he would have to complete his three year course studying and then staying for an extra year either studying some further course which lasts for 1 year or 2 work for a year. This is because you must reach 5 years residence in the United Kingdom and once he has he can apply for permanent residence sing the following link:
As to paying home (non foreign) fees at the start of his course in September he would not be eligible because he has not spent 3 years resident in an EEA country for 3 years immediately before the start of the course and because he has not done this he would not qualify at the moment but may qualify for reduced fees in the final year of his course since he would reach 3 years residence in the United Kingdom.
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