It turns out Query Monitor is, in fact, present in Customizer view. For some reason, I never once scrolled down to the bottom (or just didn’t pay attention). Just the debug/admin bar is not visible.
Also, you can do this to get the admin bar in theme customizer:
add_filter('show_admin_bar', '__return_true');
Another useful tool is WP Customizer Dev Tools (at this writing, it’s only upgraded for up to WP 4.9 on the Git branch. The wordpress.org plugin is outdated)
Keep in mind, Debug Bar and Query Monitor especially can slow down the Theme Customizer tremendously.
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