What makes it different when it is passed from the terminal?

It's not different. 

$ perl -E'$_="a"; $r=$ARGV[0]; s/a/$r/; say;' '\x41'
\x41

$ perl -E'$_="a"; $r="\\x41"; s/a/$r/; say;'
\x41

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In reply to Re^3: hex code passed from command line is interpreted literally in substitution by ikegami
in thread hex code passed from command line is interpreted literally in substitution by Allasso

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