Re-reading the spec sheet (and all the notes this time) I believe you are right. Maximum 150mA for sourced/sunk current with 25mA max for each I/O pin. The other parameters are for injected current which occurs with inputs above VDD or below VSS. My bad. I'd still choose 1 resistor value to make population even easier. It doesn't take much current to make an LED bright enough for debug purposes.
The point on the grounds is about separating the logic/processor grounds from the high voltage grounds. The coils are probably driven from a high voltage power supply. The processor and logic grounds are probably from a low voltage power supply. The grounds from both of these power supplies need to be tied together somewhere. It is best to do that near the power supplies but it can be on the board. I'm guessing the blue pill is being powered from the USB port. All of the grounds going to the switch inputs should be attached to a gnd pin that is from the blue pill. Then those big ground spades should go to the high voltage supply ground. It is tough to know how all the grounds are connected without seeing the gerbers.
Let's say a couple of coils are firing. Each one is maybe 10ish amps to be conservative (48V with 4.7 ohms for a red williams coil). That means 20 Amps is zooming through the board to the ground spades. All that current needs to go back to the ground of the 48V power supply. As it goes zooming across the board, the resistance of the trace causes the ground reference to be a higher voltage. This could cause ground bounce on the board. It probably won't matter, but by separating the grounds cleanly it can't happen.
If the board connects the gnd pin(s) from the blue pill to some pin that you can use to feed the switch closures, and then another gnd pin connects directly to big ground pin traces, everything will work perfectly. If all the grounds are connected together, it will still probably work perfect, but it isn't ideal.
Sorry for such a pitiful long winded message, but I find it difficult to explain grounds and how they should be separated and connected clearly.