Jelly, 24 bytes

iⱮṛ/;\BUz0ZUḊFŻ8¡s8z0ZḄḊ

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Jelly, 21 bytes

JBUz0ZU8,yFŻ8¡s8z0ZḊḄ

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JBUz0ZU8,yFŻ8¡s8z0ZḊḄ Main Link
J Generate [1, 2, ...] as long as the encoding list
 B Convert to binary
 Uz0ZU Reverse, transpose padding with 0, transpose, reverse (*)
 8, Pair the encoding list with the padded binary list
 y Use this to translate the message into binary strings
 F Flatten
 Ż8¡ Prepend 0 8 times (in case the list is shorter than 8)
 s8 Slice into blocks of 8
 z0Z Transpose padding with 0, transpose (**)
 Ḋ Remove the block of 8 zeroes at the start
 Ḅ Convert from binary into numbers
(*) this is a common pattern used to left-pad everything to the same length
(**) this is a common pattern used to right-pad everything to the same length -
 because we prepended a block of 8 zeroes, there is at least one sublist
 of length 8, so everything will be padded to length 8