Is this still relevant with the stickiness?

Good question; not 100% sure.  However, given Nik's recent email it does seem like the prompt correctly differentiates explicit denials vs. "bubble was hidden when navigation happened", so I think these metrics are already in place as #c1 assumes.

Can you check manually through chrome://histograms that it works as expected? Then I'm fine with the WontFix.

Thank you Mathieu; I forgot chrome://histograms existed, and it did point out a gap.

The bubble DOES correctly differentiate explicit denials vs. closing the bubble and navigating away.  However, it's not a matter of the stickiness, it's a matter of Harmony.  The [No thanks] button (when Harmony is off) is an explicit denial, while the top-right [X] close button (when Harmony is on) doesn't log anything of the sort and falls into the "bubble was hidden when navigation happened" funnel.  They also have slightly different behavior: [No thanks] hides the credit card icon in the omnibox entirely; [X] does not, just like the non-sticky version.

TL;DR: When Harmony is on, the [X] close button doesn't count as explicitly denying the prompt, just hiding it until tab navigation gets rid of it for good.