Here are the meaning of the different quota in the YouTube Data API
QPD(quota per day) - meaning the maximum numbers of request over a 24 hour period a client id is able to make to an API.
QPS(quota per second) - meaning a global quota per second for the application, meaning how many calls per second an application can make.
quota per seconds per user - meaning the number of queries a user, in the application can make.
The quota of 3,000,000 per 100 sec did not exceed the 1M QPD because you need to divide the 3M QPS to 100.
So meaning you only have 30,000 QPS or queries per second.
I hope this information helps you.