By all means modify it but purchase the parts secondhand off here, then when you come to sell standardise it then sell the bits back on here, chances are you won't lose any money.
Leave the sterio standard, its not even that bad, nobody is going to break in and nick it plus with an aftermarket you will lose your finger tip controls.
Agree with keeping the standard parts and don't do anything too permanent that you can't reverse, everything that was one mine was stripped off and sold and refitted the standard parts. Got 1k odd back from selling bits in the end.
Will disagree with the headunit though, the standard one is bloody dire compared to even low end decent stuff. And you can always take it with you and refit the standard headunit when you change cars, and a simple adapter keeps the stalk controls and screen.
All the ICE in my car has been in all 3 of my Clios and it completely reversable, only takes a few hours to strip it all back to standard and thats a full setup (front comps/rear comps/2x amps/sub/headunit/changer/ipod adapter/ainet hub/and all the assorted wiring). Can fit it all in in about 6 hours now too but i've had some practise by now lol.