I noticed some inconsistencies between EBE and vanilla texture mappings, exclusively for the up/down faces from the blocks that I've seen. These are the ones I noticed:

• The top and bottom faces for all hanging sign templates have their texture flipped horizontally.
• The bottom face for all sign templates is flipped horizontally.
• The top face for all sign templates is flipped both horizontally and vertically.
• The outside bottom face of 1-wide chests is flipped both horizontally and vertically.
• The outside bottom face of 2-wide chests is flipped vertically.
• The outside bottom face of shulker boxes is flipped horizontally.

One possible solution would be to go through the JSON file for each affected block and swap the uv values manually.
Another solution would be to change the code for how its rendered (hopefully not a big change, but I don't know the code). I noticed that in every JSON files for the sign and hanging sign templates, the u0 value is always lower than the u1 value. It's intuitive, and making the change in the code would avoid changing the order of the u values.