... can I do in-place file substitution from inside a script

If using the feature behind the -i option from within a script is what you mean... yes, you can. You can either put the -i.bak on the shebang line, or set the corresponding $^I special variable (as olus already mentioned). The latter allows a little more flexibility, e.g. you could localise the effects

#!/usr/bin/perl

use strict;
use warnings;

sub edit_inplace {
    local @ARGV = @_;
    local $^I = ".bak";
    # local $^I = "";  # no backup file
    
    while (<>) {
        s/(.*)/$1\n****************/;
        print $_;
    }
}

edit_inplace("test.txt");
[download]

BTW, even Perl doesn't do a real in-place edit (i.e. modify the physically-same file). Rather, it opens, then renames (or unlinks, when no backup extension is specified) the original file, then opens a new file with the same name — at least on Unix, where opened files continue to be accessible, even when they're no longer associated with a directory entry  (look at the inode numbers before and after to verify, e.g. with "ls -li").

You can do inplace editing from inside scripts with $^I, which is the equivalent for the -i command line option. It is described in perlvar.