I've owned the A7R, A7RII, X1D, and 645z (and for a brief period had em all at the same time). The A7RII was prob my least favorite of any of the cameras I've used to date for long exposures. I really love the X1D, but if you're thinking about one, I'd definitely try to try one out first before purchasing. It still can be a little quirky, and lens selection is more limited compared to other options, although they did just start shipping a lot of the XH adapters. The XH adapter also lacks a tripod collar, so additional lens stabilization may be warranted if using HC/HCD lenses on the X1D and doing long exposures. They seem to have a lot of future lens options in the pipeline to fill out a lens lineup, but the price point and availability are big question marks. Regarding thermal noise, the body itself acts as a giant sink which may help mitigate thermal noise.
I agree with Paul it really is head scratching why Phase hasn't a user-defeatable dark frame for long exposure. It would just take a simple firmware update unless there's something in the hardware architecture that necessitates it. Yes, there may be trade-offs in image quality, but considering the results I've gotten from Hasselblad and Pentax which don't use a dark frame, any reduction in image quality should be marginal...especially with the CMOS sensors of the today. Phase, if you are listening, this is probably the one thing that keeps me from investing in a Phase system. After getting used to no dark frame, I can't envision myself ever going back, and waiting in between shots for the dark frame to finish is not only an annoying PITA, but can cause you to miss shots in quickly changing light (ie sunrise, sunset, etc) and can cause issues in quickly changing weather scenarios.
FWIW on the 645z I used the 28-45mm, 45-85mm FA, and 80-160mm. They were all great. Disadvantage of the 645z/28-45mm combo is it's very large and heavy. The 45-85mm FA and 80-160mm FA are no-brainers IMHO since they can be found for less than $500 USD each. They lack some of the saturation and contrast of more modern lenses, and require more sharpening than I normally apply, but deliver stellar results considering the price point. A lot of the Pentax 645 A/FA lenses have a great price/performance ratio. If you're concerned about the "box" being old with the 645z, the 645z actually operates more like a 35mm dSLR than comparable MF systems, and in some ways is more advanced in the context of MF cameras. The weather sealing is also great (at least on the 645z and 28-45mm), batteries last much longer than they do on the X1D (and are much cheaper at only $50 each, and 3rd party batteries are even cheaper), and there are some other neat tricks the 645z has up its sleeve....for example there are IR sensors on the front and the rear of the camera, so you can trigger the shutter with a cheap IR transmitter from behind the camera and forgo a wired remote. It also has dual SD card slots which can be assigned to mirror one another, which I find very handy in the field when traveling and something the X1D (and maybe the GFX?) currently can't do.
There were only two things that really concerned me about the 645z. While it's built like a tank, I was worried about service if I ever needed it. There's only one US authorized service center, who told me they do not service non-US market 645z's. I bought my 645z second hand and did not know the country of origin, and Pentax could not tell me what the market of origin was based on the serial number. If it did ever need service, I'm not sure what I would've done. I also question Pentax/Ricoh's commitment to the system at this point but that's only conjecture on my part. For a long time they have had a new 45-85mm and 80-160mm on their 645 roadmap for announcement/delivery in 2017 or later, but I haven't heard or seen anything further. I asked them point blank about it on social media a few months ago and got no response. With the age of the 645z, I'd also expect new camera rumors, and haven't seen anything on that front as well.