1. There is a dedicated layer for reference designators that I include with the gerbers, that's how I printed the component placement guide in the first image. I prefer silkscreen designators but this board is just too densely packed to fit all of them on, so I figured I'd just go for a cleaner look and have none of them. I mean, just look at the area between the "CAN" and "I2C" text! Even my usual trick of "group the designators elsewhere and put a line showing what they refer to" wouldn't work, there's not enough space overall.
2. The MS621T is indeed a backup battery for the RTC and the microcontroller. It's rechargeable, so shouldn't need to be replaced unless it degrades to less than 10% of its nominal 3.0mAh capacity. According to this graph, if it's stored at 85C for 160 days at 3.1V, it will lose about 15% capacity. Unless you're regularly driving through the hottest deserts for several hours a day, with no A/C, the battery will spend almost no time anywhere near 85C. I'm also planning on keeping it charged to only 2.8V or so.
I was initially looking at supercaps, but I'm very limited on height under the cluster cover. Caps that were rated for -40C - 85C and were short enough were already >50% the price of this battery, large footprint, and not as readily available. The battery also has almost 10x the capacity. So I'm fine with making the customer pay an extra $1.50 to make my life easier.

It should also be noted that this battery only comes into effect if the car's 12V battery is disconnected, so one could say it's rather useless even including it... meh, I think it's a nice quality-of-life feature that should be present in a product like this. It will also allow me to set the time and date for you before I ship it so you won't even have to!
3. I think the input caps are pretty well placed given the pinout of the chip and location of VIN and SW. I am also willing to make slight compromises in electrical performance in exchange for aesthetics.

Here's a closeup of the layout so you can judge it further. There is an uninterrupted ground plane under it all as well. Looking at the scope traces, I think it's performing very well.
These were all captured with a 200MHz Keysight DSOX2024A, with a 14.5V input voltage and 1A load.
Input capacitor closest to the IC:
Closeup on the voltage spike (may partially be due to probing, I even bent and trimmed my ground spring to make the probing loop as small as I could)
Input ripple with the bandwidth limit enabled
SW node, measured directly across the freewheeling diode
Rising and falling edges of SW
Ripple on 5V out
4. It's the freewheeling diode, this is indeed a non-synchronous regulator. I chose this part because I needed 40V input capability (the cluster has a 24V input TVS diode, which typically clamp around 39V at their max current. The cluster 5V regulator is also rated for 40V). I also wanted a large thermal pad to increase power dissipation, and low operating quiescent current (<100uA) to make sure Pegasus will draw very little current while sleeping. 1mA is my max, but <0.3mA is my goal.
Efficiency is really only important in this application to reduce power dissipation. At 14.5V in, and 5V/1A out, I measure 90.9% efficiency, so only 0.5W dissipated. At 0.1A efficiency is only 83.2%, but the absolute power dissipated is so low it doesn't matter.
5. That's the linear 3.3V regulator.
6. That's the RTC with integrated crystal, the 24MHz microcontroller oscillator is the SOT-23-5 under the middle of the STM32.
7. Those connectors actually are 2mm pitch, not 0.1"! The camera always makes electronics look bigger.

I needed through-hole latching connectors. They also fit perfectly in the cluster cover:
Thank you for the thorough review and suggestions!
Definitely would want machine vision if I got a PnP.
It wouldn't be for producing Pegasus in quantity, I will get a board house to do that. I want a "prosumer"-grade one for prototype boards like this. Like $10k max. They have been getting better and better for cheaper and cheaper!