Not sure what current options from Shimano are for Di2 handlebar ports.
I built up an F8 for somebody a few years back. Fitted wires before anything else. Needed a special seat post internal battery mount for Pinarello aero post which had a sleeve some washers and a lock clip. I put junction box under bars (charging port is on junction box). Also needed pinarello electronic fitting kit which was plates and grommets for cable exit points on frame.
(IMHO if it is a pure dry weather bike, and unless you have loads of spare money, I wouldn't bother with DI2...just my opinion though)
Somebody else may have more up to date advice though
At least with the mechanical, you can fix it yourself, and it will be cheaper by not having to replace it, but to own over the long haul because those batteries are not cheap and for some reason only last 3 to 5 years.
But in answer to your question, you can indeed replace your mechanical system with a electronic system, it won't be as clean looking as a bike made for electronic, but it won't be that bad looking either.