Way I see it, someone in Specialized legal got over zealous
He states in his letter that it's an outside legal firm that they have contracted to chase down trademark infringements
They've been given instructions and a free hand to chase down all the infringements they can find. It sounds like within the remit they were given they went after a small business owner with an interesting life story (ex-services, PTSD, sunk life savings into dream business).
Media jump on story and it's big bad corporation vs little guy.
Specialized head office have been given a black eye by this and have done the right thing and have provided a grovelling open letter (never read owt like that before tbh)
They've given some reasoning behind their legal contractors actions, they haven't excused them or themselves.
In the meantime small shop owner has received great publicity and increased sales. Specialized have done a reasonable spin job to try and dig their way out of this. Who cares about Fuji anyway, no one buys their bikes over here anyway