I’m pretty sure you will only be a 1/4″ off if you cut 12″ off a 36″ x 48″ pan. The pans are tapered at 1/4″ per foot
But you have the right idea to make up for that difference (tiling walls with starting at the low side of pan and work your way around.) It won’t be that tough to do and shouldn’t have a problem adjusting for that. I’ve cut plenty of pans down that much
And your right, you could reduce some of that difference by shifting drain more towards the shower faucet wall and cutting the pan from both sides. Probably look better to get as close to center as you can
You will like Wedi. Its a very simple system to put together. Just measure a few times before cutting! Their pans are expensive!