Doubt about the real need for R and C on micro-controller inputs
I strongly suspect you're confusing the point of those resistors.
My money would be that a lot of it comes from trying to make the board robust under &quot;boneheaded-user&quot; situations.
The 1K resistor in both circuits is more to make it so if the connected IO pin is accidentally set as an output, it won't damage the microprocessor if the button is pressed. The capacitor in the first picture isn't /really/ needed, but it means you have to do less work in the MCU to handle switch bounce. The pullup resistor is similar, it means the switch functionality can be more easily understood without having to discuss the IO Buffer structure.
Most importantly, that is not a decoupling capacitor, so you do need decoupling capacitors, but you appear to not be asking about that.

To answer your questions:

The pull up resistance on an I2C bus is largely a function of bus capacitance, and for most I2C busses, there is a large range of values that will work. 10K should be fine for most small busses.

Again, these resistors are just to place the boot pins in a known state at power up. The choice for them is usually a matter of &quot;what resistor values am I using elsewhere, so I don't need another BoM line&quot;. It's not critical.

You should set up the crystal as the STM32F103 datasheet specifies. Various eval boards may or may not be correct, and there's some latitude in the range of connections that may be functional. A 1MΩ resistor isn't going to have much effect except for ultra low power contexts, so it may only be needed if the MCU is in a ultra-low power sleep. The 32KHz oscillator may have completely different burden requirements. Again, read the datasheet, not random eval boards.
ST Have an entire application note (AN2867) about how to set up their MCU oscillators.