The Count Repeat Instances option in AHA only governs sequential repeat instances. So it wouldn't wholly provide a way around what you are trying to do in only ever tracking against the first occurrence of a page. I haven't ever run into any issues with the page depth metric, but it does count every occurrence of the page to derive the average.
https://marketing.adobe.com/resources/help/en_US/reference/count_repeat_Instances.html
Count Repeat Instances
Specifies in ad hoc analysis whether instances are counted in reports. Meaning, if you have multiple sequential values for the same variable you can count them either as one or multiple instances of the variable.
For example, you might see repeat page reloads, which are the number of times that pages on your website are reloaded or refreshed during a single visit. This option lets you specify whether multiple hits on the same page are counted as one, or as multiple page views.