I think the reason for this slowdown is that when constructing support for the lvalue property of substr,

No, it's only done when necessary, and it's not here.

>perl -MO=Concise -e"\substr($_,1)" 2>&1 | find "substr"
5           <@> substr[t4] sKRM/2 ->6
                              ^
                              |
                             "M"odifiable => magic created.

>perl -MO=Concise -e"$a = substr($_,1)" 2>&1 | find "substr"
5        <@> substr[t3] sK/2 ->6
                          ^
                          |
                          Not modifiable => no magic created.
[download]

The time is spent creating new strings and assigning them.

Pass      1: Creates a 79,999 char string & copies it into $a's buffer
Pass      2: Creates a 79,998 char string & copies it into $a's buffer
Pass      3: Creates a 79,997 char string & copies it into $a's buffer
...
Pass 79,999: Creates a      1 char string & copies it into $a's buffer
Pass 80,000: Creates a      0 char string & copies it into $a's buffer
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It's copying (((N-1)+1)(N-1)/2)*2 = (N^2 - N) = 6,399,920,000 bytes!

However, it's possible to do what you want without copying a singly byte! Through a feature called "OOK", Perl can efficiently remove the leading chars of strings when it does so in-place.

$a =~ s/.//s;          # Remove leading char with no copying.
substr($a, 0, 1, '');  # Remove leading char with no copying.
[download]

The latter even returns the character removed! (Well, so does the former if you add a capture.)

Benchmarks:

--------------------
20,000

          Rate substr3    s/// substr4
substr3 1.61/s      --    -93%    -96%
s///    23.1/s   1336%      --    -44%
substr4 41.2/s   2460%     78%      --

--------------------
40,000

           Rate substr3    s/// substr4
substr3 0.884/s      --    -96%    -98%
s///     23.1/s   2509%      --    -45%
substr4  41.6/s   4606%     80%      --

--------------------
80,000

           Rate substr3    s/// substr4
substr3 0.445/s      --    -98%    -99%  (warning: unreliable count)
s///     23.4/s   5162%      --    -42%
substr4  40.1/s   8897%     71%      --
[download]

The rate is the number of times 80,000 chars can be processed per second. Notice how the 4-arg substr and s/// aren't affected by the length of the input?

Benchmark code