So, i believe your original assumption is correct - they used forced perspective. If you pay very careful attention to Alice's feet during the drink me/shrinking scene around the 10-11 minute mark she is actually standing on some sort of platform/board. Also there is something strange that happens at around 10:56 when Alice's hand crosses with the table. I was also able to find a promotional photo from the film that shows the shadows, and the board a little more clearly.
Later when she is in the White Rabbit's house she: enters the room, crosses towards the left and you see her shadow on the left/fireplace, then she moves back the right - all one shot. There is a cut as she places the bottle down, and when we cut back we are in a different shot/set. If you pay attention to how dark the shadows on the wall are before the bottle cut/insert shot, then afterwards they clearly do not match.
I hope this helps! please let me know if you have any other questions.