I feel that complex workflows are best served by dedicated integrations, but it takes time for developers to build each integration natively into a product. We launched https://kloudless.com to simplify the process for app developers to natively integrate an entire category of SaaS services at once (I'm a co-founder).

Ignoring platforms like Salesforce, some of the "product" apps that we see adopting native integrations instead of directing users to Zapier include apps that require:

1) synchronous interactive integrations and not just background automation. e.g. a user pulling a lead from Salesforce into a marketing app.

2) complex/multi-step integrations that offer way better UX and much lower support costs to just build natively for users.

3) integrations as a competitive differentiator, or without requiring users to pay for third-party tools.

4) integrations without an API of their own to integrate to.

That said, there are always a long tail of apps and use cases so I'm certain we'll see more specialized tooling pop up to handle specific complex workflows.