I had the same problem with our STM32L4 LoRa boards (www.radioshuttle.de). I have used an external 1M to GND pulldown for our Turtle board to get the noice with wakeups solved. Now I am at about 1µA.
I had as well the same problem with an extern SPI Flash chip, same solution.
It was as well very hard for me to find the source the the problem, fingering the pins was helpful to see deep sleep power changes.
Regards Helmut