Before the 3.3V comes to the MCU, there might a leakage from this voltage divided VIN and through the ADC input pin of the MCU, through it's ESD diode and to the MCU's 3.3V rail.
I'm using solution like your since years without any extra isolation.
1.
Why you get such high voltage at output of your divider?
I was using only 2 MCU families and both had internal voltage references for their ADC in a range of 1V that are better references than using VCC as reference.
So my divider is 100k+(3k3 || 1n) to be measured in 0..1V range for VIN up to 30V.
2.
Even you get at divider output voltage comparable with 3V3 VCC I would not be afraid of powering MCU by 470k resistor.
3.
I understand that VCC comes from the same VIN.
The voltage at SEN_ADC11 rises with time constant around 10ms. Do the step down is not faster than this?