It is possible that your issue isn’t just MongoDB related, more about your cloud provider related. In your first message you didn’t mention that you use Linode’s virtual servers, but that could be the clue. Many VM providers limit IOPS on their products based on tier (which is often memory based). What you experienced with your testing kind of shows that. Those Nanode’s and lowest 2 core computers, they seem to be shared hosting. Dedicated VM’s could have more IOPS, and startup times could be a lot faster.
I haven’t tried out MongoDB on real hardware, or big databases, so I don’t have exact tips for you. But if you have hardware where you could try out starting up your MongoDB, it could verify those usage restrictions. Or you could find it from some more detailed specs sheets of Linode. I know that Google Cloud & AWS at least have such resource restrictions in their VMs, and I/O intence products need more juice than they would otherwise require CPU/RAM.
That could potentially be selling point of MongoDB Atlas, if wanting to use hosting provider anyway, why not use theirs, and get their support making sure things are working as it should.