Vyxal, 16 bytes
b8∆Zf0LbLẇvBꜝ‹İ∑
b # Convert each from binary
8∆Z # Pad each to length 8
f # Flatten
ẇ # Split into chunks of length...
0LbL # Length of the encoder string, in binary
vBꜝ‹ # Convert each from binary, remove 0s and decrement
İ∑ # Index those into the encoder and sum
emanresu A
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