Does the NEC (or anyone else) limit the size of a branch CB in relationship to the main CB, other than it can't be bigger? i.e. can I have a 100A branch in a panel with a 100A main? The load is very low so I don't have any issues there.
If it isn't an Article 700 or 701 application or an elevator or a hospital, then I don't seen any reason why it is a code violation.
Instead of the 100A distribution breaker, why not use feed-through lugs, and use the main CB as your protection?
In general a branch device can be any size allowed by the panel, even if it is larger than the main. Of course, as Ron mentioned, there are a few areas where branch and feeder devices must coordinate.