but when comes to little-endian [...] it is still auto add a carriage return in front of a line feed

No it doesn't. Either it adds CRs before LFs or it doesn't. It doesn't know or care how the string was constructed. Something else changed.

open TARGET_FILE, '>', 'foo' or die;
binmode TARGET_FILE;
my @list = 10;
my $outputstring = pack("v*", @list);
print TARGET_FILE $outputstring;
[download]

>perl script.pl

>debug script.out
-rcx
CX 0002
:
-d100 l2
0B02:0100  0A 00                                             ..
-q
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PS — Why are you using a global variable (as in TARGET_FILE) for your file handle instead of a lexical? The former hasn't been required for 8 years.