The non-technical reason is that these are usually owned by different teams in your org (after you mature beyond a 5-person startup).

The technical perspective is that things like wildcard subdomains (e.g. to support yourcustomername.example.com), or DNSSec if your compliance requires it, etc. cause an extra burden if done for these two use-cases at a time.

> can't easily click

Http pages don't have problems with having a link to example.net from within example.com. Or the opposite. Seems like an unrelated problem.

One potential reason is that marketing teams often want to do things that are higher risk than you may want to do on your main application domain. For example, hosting content (possibly involving a CNAME pointing to a domain outside your control) on a third party platform. Using a framework that may be less secure and hardened than your main application (for example WordPress or drupal with a ton of plugins) using third party Javascript for analytics, etc.