This feels like a case in the gray area. On the one hand, companies need to declare certain stuff out of scope - whether they know about it and are planning to work on it, or consider it acceptable risk, as the point for the company is to help them improve their security posture within the scope of the resources they have to run the bug bounty program. What's weird here is that the blog author found an email problem that wasn't really in that DKIM/SPF etc area, and Zendesk claimed that exemption covered it. Without a broader PoC to show how it could be weaponized, it's hard to say that Zendesk was egregiously wrong here - the person triaging just lacked the imagination to figure out that it would be a real problem. Hell, later in the write up we learn Zendesk does do spam filtering on the inbound emails, and so it's not crazy to think a security engineer reading the report may assume that stuff would cover their butts, when it failed miserably here. (A good Engineer would check that assumption though)
That said putting my security hat on, I have to ask - who thought that sequential ticket ids in the reply-to email address were a good idea? they really ought to be using long random nonces; at which point the "guess the right id to become part of the support thread" falls apart. Classic enumeration+IDOR. So it sounds like there's still a potential for abuse here, if you can sneak stuff by their filters.