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Bash (203203, 197 chars)

#!/bin/bash
r=" ▝▘▀▗▐▚▜▖▞▌▛▄▟▙█";while▝▘▀▗▐▚▜▖▞▌▛▄▟▙█" IFS=IFS=;while read -r m;do IFS= read -r n;forn o;for((l=${#m}>${#n}?${#m}:${#n},i=0; i<l; i+=2)){
printf -ve %-2s "${n:i:2}" "${m:i:2}";e=${e//[^ ]/1};o+=${r:2#${e// /0}:1};};echo "$o";o=;done"$o";done

or

r=" ▝▘▀▗▐▚▜▖▞▌▛▄▟▙█"
while IFS=
while read -r m; do
    IFS= read -r n o
    for ((l=${#m}>${#n}?${#m}:${#n},i=0; i<l; i+=2)) {
        printf -ve %-2s "${n:i:2}" "${m:i:2}"
        e=${e//[^ ]/1}
        o+=${r:2#${e// /0}:1}
    }
    echo "$o"
    o=
done

Bash (203 chars)

#!/bin/bash
r=" ▝▘▀▗▐▚▜▖▞▌▛▄▟▙█";while IFS= read -r m;do IFS= read -r n;for((l=${#m}>${#n}?${#m}:${#n},i=0; i<l; i+=2)){
printf -ve %-2s "${n:i:2}" "${m:i:2}";e=${e//[^ ]/1};o+=${r:2#${e// /0}:1};};echo "$o";o=;done

or

r=" ▝▘▀▗▐▚▜▖▞▌▛▄▟▙█"
while IFS= read -r m; do
    IFS= read -r n
    for ((l=${#m}>${#n}?${#m}:${#n},i=0; i<l; i+=2)) {
        printf -ve %-2s "${n:i:2}" "${m:i:2}"
        e=${e//[^ ]/1}
        o+=${r:2#${e// /0}:1}
    }
    echo "$o"
    o=
done

Bash (203, 197 chars)

#!/bin/bash
r=" ▝▘▀▗▐▚▜▖▞▌▛▄▟▙█" IFS=;while read -r m;do read -r n o;for((l=${#m}>${#n}?${#m}:${#n},i=0; i<l; i+=2)){
printf -ve %-2s "${n:i:2}" "${m:i:2}";e=${e//[^ ]/1};o+=${r:2#${e// /0}:1};};echo "$o";done

or

r=" ▝▘▀▗▐▚▜▖▞▌▛▄▟▙█" IFS=
while read -r m; do
    read -r n o
    for ((l=${#m}>${#n}?${#m}:${#n},i=0; i<l; i+=2)) {
        printf -ve %-2s "${n:i:2}" "${m:i:2}"
        e=${e//[^ ]/1}
        o+=${r:2#${e// /0}:1}
    }
    echo "$o"
done
edited body
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Bash (234203 chars)

#!/bin/bash
r=" ▝▘▀▗▐▚▜▖▞▌▛▄▟▙█";while IFS= read -r m;do IFS= read -r n;for((l=${#m}>${#n}?${#m}:${#n},i=0; i<l; i+=2)){
printf -ve %-2s "${n:i:2}" "${m:i:2}";e=${e//[^ ]/1};o+=${r:2#${e// /0}:1};};echo "$o";o=;done

or

r=" ▝▘▀▗▐▚▜▖▞▌▛▄▟▙█"
while IFS= read -r m; do
    IFS= read -r n
    for ((l=${#m}>${#n}?${#m}:${#n},i=0; i<l; i+=2)) {
        printf -ve %-2s "${n:i:2}" "${m:i:2}"
        e=${e//[^ ]/1}
        o+=${r:2#${e// /0}:1}
    }
    echo "$o"
    o=
done

Bash (234 chars)

#!/bin/bash
r=" ▝▘▀▗▐▚▜▖▞▌▛▄▟▙█";while IFS= read -r m;do IFS= read -r n;for((l=${#m}>${#n}?${#m}:${#n},i=0; i<l; i+=2)){
printf -ve %-2s "${n:i:2}" "${m:i:2}";e=${e//[^ ]/1};o+=${r:2#${e// /0}:1};};echo "$o";o=;done

or

r=" ▝▘▀▗▐▚▜▖▞▌▛▄▟▙█"
while IFS= read -r m; do
    IFS= read -r n
    for ((l=${#m}>${#n}?${#m}:${#n},i=0; i<l; i+=2)) {
        printf -ve %-2s "${n:i:2}" "${m:i:2}"
        e=${e//[^ ]/1}
        o+=${r:2#${e// /0}:1}
    }
    echo "$o"
    o=
done

Bash (203 chars)

#!/bin/bash
r=" ▝▘▀▗▐▚▜▖▞▌▛▄▟▙█";while IFS= read -r m;do IFS= read -r n;for((l=${#m}>${#n}?${#m}:${#n},i=0; i<l; i+=2)){
printf -ve %-2s "${n:i:2}" "${m:i:2}";e=${e//[^ ]/1};o+=${r:2#${e// /0}:1};};echo "$o";o=;done

or

r=" ▝▘▀▗▐▚▜▖▞▌▛▄▟▙█"
while IFS= read -r m; do
    IFS= read -r n
    for ((l=${#m}>${#n}?${#m}:${#n},i=0; i<l; i+=2)) {
        printf -ve %-2s "${n:i:2}" "${m:i:2}"
        e=${e//[^ ]/1}
        o+=${r:2#${e// /0}:1}
    }
    echo "$o"
    o=
done
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Bash (234 chars)

#!/bin/bash
r=" ▝▘▀▗▐▚▜▖▞▌▛▄▟▙█";while IFS= read -r m;do IFS= read -r n;for((l=${#m}>${#n}?${#m}:${#n},i=0; i<l; i+=2)){
printf -ve %-2s "${n:i:2}" "${m:i:2}";e=${e//[^ ]/1};o+=${r:2#${e// /0}:1};};echo "$o";o=;done

or

r=" ▝▘▀▗▐▚▜▖▞▌▛▄▟▙█"
while IFS= read -r m; do
    IFS= read -r n
    for ((l=${#m}>${#n}?${#m}:${#n},i=0; i<l; i+=2)) {
        printf -ve %-2s "${n:i:2}" "${m:i:2}"
        e=${e//[^ ]/1}
        o+=${r:2#${e// /0}:1}
    }
    echo "$o"
    o=
done