As a Fabia VRS owner (mk2 1.4 TSi to be fair) and someone who nearly bought a Mk1 in late 2003 I'll post in here and try and be unbiased.
The MK1 Fabia VRS is an ok car. It isn't fantastic, it isn't totally awful. It, in my opinion, shouldn't command a huge price premium, other than a premium over other Fabia's of the same age due to its 'standing' in the range. In short, I think that 4k is a LOT for a nearly 10 year old car with nearly 100k on the clock.
It handles ok, but felt quite hard and high to me, below the handling you'd get in a Fiesta or a Focus... I drove an Ibiza PD130 Sport at the same time but couldn't tell huge amounts between them. The Seat felt a bit more youthful, but that was down to interior design. I ended up buying a 2003 Focus TDCi 115 Zetec instead of the Fabia.
I'll comment on the MPG. You won't get 60mpg tootling to the shops. On a long commute, when the engine is warmed up, if you have cruise control on, its on the motorway, and your doing 60 ish you might do. You'll end up in the high 40's, low 50's depending on variation on those factors, significantly lower if your doing 70-80-90 etc.
I personally think 4k is a lot of money for what you are getting, and I recently spent out on a well specced 2011 Fabia VRS Estate. I got destroyed for doing it, but it was one of the only cars we found that met our needs. Would I buy it again? Almost certainly. Would I have got less stick if I'd spent the same money on a year older Octavia VRS? probably.
Fox is right that for a commuting car the Toledo would be a good option. Both that and the Bora (to a lesser extent) offer a good value for money car. It would probably be better suited to your needs, but I don't feel you have given us much to go on for suggesting another car.
How many miles is your commute? you might find that a Petrol will cost less and get you a newer/better condition car and not work out much if indeed at all more expensive. On a long run I can get mid 50's on my Fabia VRS, and thats a 180 BHP Petrol ! Granted its a newer engine design, but you'd be surprised what Petrols will manage.
Regarding the Remap, that will hit your fuel economy if you 'use' the remap. You hear varying things about how far you can push a PD130 engine. Someone in my office claims to have just over 200 bhp, but he has a hybrid turbo, different exhaust, different intake, and some 'custom' remap. I don't doubt it must be quite a reasonable drive now for straight line oompf, but he had to get a different cluch fitted to cope with the loltorqs. Personally I'd get a standard car.