I have factory navigation. Having tried to live with it for a few weeks, I personally would prefer just about any aftermarket option over it. (And I don't even really need to use it very often at all.) Extremely clunky interface, no touchscreen, very dated-looking maps, fonts, etc. I gave up on it and just started using Google's free turn-by-turn on my phone.
Besides setting the time and date, fuel consumption/range is the only other thing I've seen on the OBC menu that I would use. And as I said above, an app like DashCommand is going to give me much more detailed information than the factory OBC through the current head unit. Other than that, I'm really not sure what else I'm missing that would be a big loss.
I have seen some other dash kits, including a very nice-looking but completely comical price-wise model from Japan...literally twice the cost of the new head unit I'd be putting in the middle of their lovely piece of plastic:
BMW x5 E53 Double DIN Dash Kit Factory Nav | eBay
The Janus is nice, and maybe I'll change my mind after I live with the Metra kit for a while. But right now I'd rather put the extra $120-130 different in cost toward a better five-channel amplifier. Or a JL Audio Stealthbox to replace the factory "subwoofers".
Do you have any pictures of your custom E39 kit? I have to say I'd probably do more harm than good if I tried a custom job like that. But if yours looks good enough, it might inspire me to try to overcome my craftsmanship deficiencies.