It's in, and it sounds MUCH better than the factory system. The JL amp is mounted in the driver's side rear panel and looks good. I was surprised how small it is, given how much power it provides. It's probably too much for the puny factory subs, so a JL Stealthbox will be going in on the other side at some point.
They had to modify the Metra kit to get it to fit, so there's a sort of gap at the bottom. They did a decent job filling it in, but it still doesn't look very good. I ordered this kit, which looks like the Janus one:
BMW 5S E39 Double DIN 2 DIN D DIN DDIN Bezel Kit | eBay
I also ordered some matte graphite vinyl. If it matches the factory trim well enough, then I might wrap the whole thing or maybe just the top part of the bezel. Not sure how good it would look butting up right next to the dark poplar trim on either side. I think the contrast looks good on the doors, but there is some black buffer in between in those areas.
The only issue is I've noticed some very light intermittent noise/static in the system. I'm going to take it back up there and have them fix that issue once I get the new kit. That way they can swap them out at the same time. I'll post some pictures when that's done.