Based on your comments you are trying to see what changes a plugin is performing in the core and contrast them to what the core does. First thing to consider is that there WILL be differences, otherwise the core would already behave as the plugin :P Anyway, I understand you just want to check if the plugin is, for instance, missing something.
As I explained in the other answer... there is no way to be 100% sure that everything will be there as the core expects because you're actually modifying the core's data. The more high-level functions you use the better. In other words, the least plain SQL you use, the better.
But specifically answering this question, the best approach to follow would be to turn the performance debugger (QA_DEBUG_PERFORMANCE) on by setting it to true in your qa-config.php file. This will give you a list of all queries that are being run. If you only see one epic and horrible query and just a few others then you have QA_OPTIMIZE_DISTANT_DB enabled. This will mask all the queries generated with selectspects. Maybe you want to keep it enabled to focus in the queries that actually change data (such as updates, deletes and inserts). But that's up to you.
Then you'll have to perform the tests without the plugin in the folder (or just rename qa-plugin.php to anything else!). Take notes. Put the plugin back again. Run the tests. Take notes. Compare. If that was your intention... I'd advise you to get a comfortable chair :)