Can you please specify your Kibana version?
I've seen that we have few bugs going around related to Duration formatter, I've seen also that reordering the metrics can solve the axis problem: try to rearrange the mertics moving the Average atmicro one as the first in the list.
My Kibana version is 6.3.2.
I tried switching the metrics, then it goes well for my duration value but it messes with my other metric. So I think it is more about a 2nd metric matter more than format issues.
Here an example of what it does when I put my count agg at 2nd place:
yes, unfortunately that's exactly the bug specified in the github issue before.
Have you tried to use Visual Builder for that? I think you can add multiple series, specify "separate axis" for one series and you can specify the duration format on the option panel (from ms to seconds with 3 decimal places).
I've run a test on my 6.3 version and seems to correctly handle that