I've learned that SOAP is a relative of SMTP.

That's certainly not how I would phrase it. Perhaps you can explain how you think they are "relatives"?

Specifically, adiosing the lines:

The following optional modules were not available:

    * SOAP::Lite is not available.
      This module is required for the query() method. If you do not
      intend to use this method, SOAP::Lite is not needed.

It is not necessary to install these now. If you decide to install the
+m
later, this software will make use of them when it finds them.
[download]

I never use Module::Build when I have the choice but it looks to me like that is Module::Build boilerplate. The only way you are going to remove this is to change the distribution's dependencies such that SOAP::Lite is no longer a recommended dependency.

Does the # commented line represent a test?

No. It is a diagnostic message output by the test script which is not part of TAP. You can safely ignore it if all your tests pass. I think this means we can safely bypass Q3, Q4 and Q5. :-)

Q6) Are there more subtle ways to do this?

Dear $DEITY I hope not. That's an unattended privilege escalation and is 100% asking for trouble. Don't even go there.