Installed mods: Thaumic Augmentation 2.1.9 and its dependents

Bug: Celestial Observer cannot pull from vanilla chest due to the chest being smaller than one block

Demonstration:

Two celestial observers with different block size containers, a chest and a dispenser.

The first observer doesn't pull from the chest

The second observer does pull from the dispenser

Work-around:
I had a similar issue.
I resolved it by nudging the position of the observer and having a solid block to rest it on.
it seems it needs to be lined up just right so that it is mostly over the chest, but at full block height.
Using this method I was able to use this with double chests. (not shown, placing a chest on one of the cobblestone blocks that the observer's hitbox is not colliding with also successfully received output scans as per the thaumonomicon)