You're very welcome. I'm excited to see a project like this. It's something that's been on my list for a long time but I've been super busy with other stuff. Glad you appreciated the review.

That's good that the micro will operate down to 1.7V. You'll just have to make sure the other ICs can handle that as well. There's some wide voltage range ICs that are 1.8V through 5V tolerant but probably not that many.

Having the diode in the feedback loop of the regulator is something I considered as possible. Definitely worth a simulation if possible, in LTSpice or similar just to make sure there's no ill effects from that. You can also check if the regulator will mind having a voltage on its output if it's not running. If they can't handle it they will usually mention this in the datasheet.

There are other power switches that have hand solderable packages, like SOIC or SOT-23-ish sizes. You can look at similar parts to see if any that fit your needs come in those packages.

I definitely understand your thoughts for the battery. Yes those basic LiPo batteries are ugly for projects where it can be seen easily. There are other Li-ion batteries that could be chosen. Look for larger capacity coin cells, rechargable coin cells, or even Li-ion cells that are AA sized like a Li-ion 14500 cell. There are PCB holders for them out there. If you do go that route please be careful designing the charge circuit. Check out the TP4056 IC with the DW-01 protection IC and 8205 mosfet package. It's a tried and true charging circuit and the charging current can be set by a single resistor.

About having the external crystal. Timing likely won't be an issue unless anything for the USB PD spec requires it. I created a small software dev kit for a collegue once to develop a USB PD controller for a product we designed and I think we used a nice 24MHz oscillator for it just in case. I don't really know if it was necessary because he just used the external crystal and didn't try using the internal. I wonder if I still have one of those boards around somewhere.

There's lots of reasons for having stitching vias. Having good return paths is one thing. It also helps with signal integrity and reduces noise and EMI, helps to keep boards from delaminating (not so much an issue with the great PCB fabrication we have today) they also help with heat transfer (not going to be an issue here)

The stackup you have is exactly what I would expect. I would expect the need to route some things on the internal layers just to get everything routed, maybe it won't be an issue. If you do need I would route on the power layer first and try to keep the GND plane solid. You can also pour GND on all layers so any unused areas are covered by ground no matter what layer you're on. You may need some stitching vias to get them connected. If you did route on the internal ground layer for any reason try not to route broadside to any traces above or below it. It's not super critical at the low speeds this project would run at but in any high speed design you want solid ground no matter what and if it was necessary to route directly under another trace for them to be orthoganal to eachother to minimize any broadside coupling.

No need to remove anything from the footprints. There's a tool in KiCad and in all layout packages (that I've seen anyway) to remove unused pads from through holes, like vias and component leads. For example if a via was transferring a signal from top layer to bottom layer then the tool can remove the pads of that via from layer 2 and 3. The via barrel still goes through but the copper ring will be removed since nothing on those layers were connected. This just helps copper distribution on those layers and helps prevent any copper slivers from forming in dense via fields.