Right, so you think of your packages as function suites.

package Functions::Base;
use strict;
use Exporter;
our @ISA         = qw(Exporter);
our @EXPORT_OK   = qw(func1 func2 func3);

sub func1 {
    print "hello";
}
sub func2 {
    print "kind";
}
sub func3 {
    print "world";
}

return 1;
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and

package Functions::Alternate;
use strict;
use Exporter;
use Functions::Base (@Functions::Base::EXPORT_OK);
our @ISA         = qw(Exporter);
our @EXPORT_OK   = (@Functions::Base::EXPORT_OK,
                    qw (funcx funcy)
                    );

# func1 is going to be replaced with our own
no warnings 'redefine';
sub func1 {
  print "goodbye";
}

# func2 is going to be replaced with our own
sub func2 {
  Functions::Base::func2();
  print "(haha)";
}
use warnings 'redefine';

# func3 is reused from orig::functions unchanged

# a couple new functions
sub funcx {
  print "new x";
}

sub funcy {
  print "new y";
}

return 1;
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and

package Functions;
use strict;
use Exporter;
use Functions::Base qw(func1 func3);
use Functions::Alternate qw(func2);
our @ISA         = qw(Exporter);
our @EXPORT_OK   = (func1 func2 func3);
return 1;
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so for subroutines

use strict;
use Functions::Base qw(func1 func2 func3);
func1;
func2;
func3;
print "\n";
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or

use strict;
use Functions::Alternate qw(func1 func2 func3);
func1;
func2;
func3;
print "\n";
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or

use strict;
use Functions qw(func1 func2 func3);
func1;
func2;
func3;
print "\n";
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I'd also note that by printing the functions which contain print statements, you are uselessly printing the functional return values, which will be 1. Thus, you are appending 1 to the end of your outputs for each call.