Since The Register is a British site, and is also known for often being somewhat tongue in cheek, there really isn't anything to read in to their use of the word.
"There is little that irritates scientists more than the idea of the "boffin". This century-old meme has at least two flavours: the befuddled, bespectacled, bad-hair-day (or no-hair-day) man, socially inept but somewhat cuddly (think Doc in Back To The Future); and there is the more sinister iteration: the equally dishevelled but cold, arrogant and/or mad male meddler, bent on no good (think Rotwang in Metropolis).
"Neither of these versions is remotely flattering, and neither bears any resemblance to reality."