aws-missing-tools VS aws-mfa

I'm not exactly sure what you're asking. But, if you are using AMIs and an autoscaling group, all you need to do is to update the AMI (launch configuration) for your autoscaling group, and then run this script that I linked to above. This script will automatically gradually roll out and replace the instances that are on an autoscaling group.

I will tell you that some tools like sceptre and terraform barf using a profile with mfa like this and I ended up using aws-mfa: https://github.com/broamski/aws-mfa and run this for example to create a "dynamic" runamok-power profile:

I use MFA so store a long term key that is used to generate a temporary key. I use this tool to do the mfa: https://github.com/broamski/aws-mfa

I too, struggled with aws-vault and eventually gave up and use https://github.com/broamski/aws-mfa. If you want to take it one step further you can use oathtool and store the totp key in the encrypted vault of your choice. That is still MFA but if you store the factors on the same system you will need to decide about that risk before going the oathtool route.

The built in CLI MFA solution sucks if you have a workflow that relies on named profiles. We use them heavily at work and implemented aws-mfa to make it so that all of our stuff could work without adopting ridiculous workflows.