I think I've solved all my problems with power consumption being somewhat higher than I hoped. Previously the calculator consumed 40-55 uA of current from the 3V battery, which was to my knowledge a bit on a higher side of what one should expect from STM32L476 in STOP mode.
I discovered that in fact the STM32 was put into STOP1 mode, while there is a more economic one, STOP2, which, however, takes longer startup time (does not matter in my case). STOP2 is activated with the extended HAL function
That solves my problem. With STOP2, the STM32 itself draws only 2-3 uA, and that increases to 10-12 uA with LCD on. This must be sufficient to run the calculator from a single CR2032 for several years.
Another small fix I had to do is to add an electrolytic capacitor of 47 uF in parallel to the battery. This fixes occasional resets of the calculator while waking up. As far as I understand, this could happen when the 3V->5V DC converter is powered up and starts to charge the capacitor C2. With the battery being not fresh enough, this could deplete the voltage for a short time below the minimum needed for STM32 to operate, causing it to reset when the voltage is back to normal. Adding extra capacitor with the value a few times higher than C2 fixed this.