Snapshot.pm is just a text file with a list of modules inside. Now, Perl happens to be a tool that was created with text manipulation in mind. Therefore, why don't you use it as a filter?

The quick way:

$ perl -i.bak -ne 'print unless /(?:Module1|Module2)/' Snapshot.pm
[download]

The classic way:

#filter_snapshot.pl
use strict;
use warnings;
my @exclude_modules = map {chomp;quotemeta($_)} <DATA>;

FILTER:
while (<>)
{
   for my $excluded (@exclude_modules)
   {
        next FILTER if /$excluded/
   }
   print ;
}

__DATA__
module1
Module2
Module3::SubModule
Module4
[download]

Invoke it as

$ perl filter_snapshot.pl Snapshot.pm > New_Snapshot.pm
[download]

An even more quick/classic way: use a text editor :-)

Here's why I'm suggesting that - it's better to test out any applications depending on that autobundle first. The best way I've found to build an autobundle is to install the base, then run your stuff. You're probably missing a module, so you install it. Keep running your test suite (you have one, right?) and installing missing dependencies until your suite runs. Then, autobundle and go home. :-)

"Here's why I'm suggesting that - it's better to test out any applications depending on that autobundle first. The best way I've found to build an autobundle is to install the base, then run your stuff. You're probably missing a module, so you install it."
But i won't be missing a module in Perl v5.8.6 if that module is already installed in v5.6.1 (i have both version of perl installed) AND if that module does NOT have XS/C extension, right?

Different @INC's. You can copy one to another, but they're not considered the same. Reason being is that even PurePerl can have Perl version dependencies. For example, PDF::Template installs differently depending on if you're using 5.8+ vs. pre-5.8.

Being right, does not endow the right to be rude; politeness costs nothing.
Being unknowing, is not the same as being stupid.
Expressing a contrary opinion, whether to the individual or the group, is more often a sign of deeper thought than of cantankerous belligerence.
Do not mistake your goals as the only goals; your opinion as the only opinion; your confidence as correctness. Saying you know better is not the same as explaining you know better.