Given the signal speeds involved, you can send it to JLCPCB as is and it'll probably be fine. You took obvious care with the USB data lines ... the other buses are slower.
I am suspicious of R25. What's the bus between the ATmega and the RTC? I2C? If so it should be pulled up correctly. Those RTCs often have other lines too, like for alarms ... good to connect those as well. In general, anything you're unsure of, connect it or break it out to test points or to footprints for 0 Ohm resistors. That's how you can maximise the odds of easily being able to salvage the board when you find problems like for example UART TX and RX not being crossed over.
The ground plane on the bottom layer is broken up by all the traces. Try to keep it more connected. Simplistically, current will want to flow from the GND pins of the ATmega, 7-segment LEDs, etc. back to the USB port ... and it will try its damndest to do this as close as possible to the path the current originally took from the USB port to those devices' VCC pins. If you don't let it take a nice short path, you get EMI and other problems ... but again, mostly at higher frequencies. Robert Feranec has some good videos explaining this, as well as about a hundred short tip videos for PCB design ... highly recommended.
Also if you intend to use solder paste I highly recommend you order a stencil with your PCBs to make assembly easier. It doesn't have to be a huge one in a frame ... order a small one without frame, it's not expensive and it's fine for a few boards.