You seem to have the structure:

if a and b and c then do...
if !a then do...

Which, if I'm not messing up my logic analysis, can be simplified to:

if !a or b and c then do...

Both functions should be simplified down to:

sub alphabeta {
    my ($self, $test) = @_;
    ...
    foreach ...
        if (!... || ... && ...) {
            push @foo, [ @bar ] if !$test || $self->{baz} eq $gamma;
        }
    }
    push @foo, [ @bar ] if !$test || $self->{baz} eq $gamma;
    return \@foo;    
}
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Then you'd just call it with the second value turned on if you wanted $self->{baz} tested.

I am of course also little confused as to what the second push @foo, [ @bar ] is there for.