My Elegance has been very reliable. I think the Mk3 Octavia is as good as any new car will be for reliability. You can always rely on the internet to turn a few unfortunate issues into epidemics, but as that isn't happening here, I think that is a pretty good endorsement.
On the spec - I would say think very, very carefully about the Nav and Canton if you think you might like them. In terms of aftermarket Nav, you can't just pull the headunit any more and fit an aftermarket one - it's fully integrated into the car. And for £500, you wont get close to the Canton. I've not heard the Canton, but it gives you an amp with DSP, centre speaker, sub, and upgraded speakers all round - I'm sure it sounds pretty decent. I have done the whole aftermarket stereo thing. Even DIY, the components alone to make a remotely impressive sound would be £1000 - £250 amp, £250 front speakers, £250 DSP, £250 sub - plus cutting up your car and running wires. It might sound better - if you really know what you're doing - but it is not difficult to spend a packet and make it worse!!!