5 door practicality goes hand in hand with DSG convenience, IMO that's why it is the rarer combination. Someone buying a 3 door is generally more interested in performance than practicality (as it is less practical than the 5 door) and is probably more likely to favour a manual box.
Even so, I don't think it will be a dealbreaker, but the enhancement of DSG on guaranteed future value (GFV) of only £300 for what is a £1415 option suggests to me that DSG isn't that highly sought after. 5 doors on the other hand is.
You won't get caned for having 3 doors, but when buying on solutions and changing every 3 years, 5 door cost (£655 on list) is effectively nil as it costs £10 a month more than 3 doors (£350/35 months) but enhances the GFV by over £400 (so you get your money back).
Either way your 3 door DSG won't be hard to pass on later, it'll be a smidge less popular on the used market, but for a car that'll be sought after in many combinations you won't have any bother getting rid of it.