While I cannot provide you the exact chemical differences between raw and boiled linseed oil, there is a chemical difference. The primary difference is the drying time in BLO is altered (shortened) via chemical additives.
And boiling is a misnomer. It is not actually boiled. I remember reading a long time ago that one of the original methods of altering the drying tinme of raw linseed oil was to inject nitrogen gas into the vats of the raw linseed oil. Workers misinterpretted the bubbling action as boiling, thus the term 'boiled' as applied to the product. Whether that is urban legend or not is up to debate. Makes for a good story tho.
And, for all you science geeks and non-geeks alike, the question I use to test the quality my kid's science teachers and their education is: Did you know that you can boil water until it freezes? If you can understand that and correctly answer why, then I know you understand the true principle of boiling and what actions can effect or affect the process.