Earlier this month, Bing launched the Site Scan feature in Bing Webmaster tools. But there was an issue with it, where it thought pages with the Base HTML tag were pages that 404ed. Bing has resolved the issue and should now properly scan and audit those types of pages going forward.
When the tool launched, if you used the base HTML tag on your pages, Bing would think the page did not exist. At least the site scan tool thought so, I doubt Bing's crawler felt that way.
But Bing said over the weekend that this issue is now resolved with the Site Scan tool:
Thanks Martin we missed indeed this one🙏 that's fixed now.
— Bing Webmaster Team (@BingWMC) June 14, 2020
Forum discussion at Twitter.