If you do it yourself and know what you're doing, your own will be better and easier. But yes, the electronics package can be made to work with whatever you want to do except amp up your speakers (well maybe you could, with alot of line-out convertors? I'd have to look into it), and if you add a subwoofer you will have to adjust the gains/bassboost through the amp since the stock nav screen won't have any of those options.
Don't buy any factory equipment that you plan on upgrading, IMO.
agree if you know you plan on putting a system in just go with the basic audio system but if you have it already yes it can be made to work there is a lot more work that goes into tuning your system but it can be done
i have done subs and amp for door and rear speakers 1 4 channel line converter at the deck and 1 2 channel in rear for subs lots of tuning but sounds great now