It just strikes me that as substr is a built-in, it could accept undef as a legitimate parameter.

Actually, it's only build-ins (be them functions or operators) that trigger this warnings. Which you have to actually enable to see them.

Why shouldn't this warn, but any of the following should:

$x = 3 + undef;
printf "%s", undef;
undef =~ /./;
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The warning is to catch cases like:

$x = expression unexpectedly returning undef.
substr $y, 1, 2, $x;
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One could argue that using a literal undef shouldn't trigger the warning (after all, then the programmer is explicit), but I don't think that information is easily available at the moment the warning is triggered. And the programmer may as well write "" or 0 anyway, saving some keystrokes.