When Font Setting changes are made through Queries>Properties Dialog, the changes are not reflected in the MapWindow.
Here is a workflow that demonstrates the issue:
Notice that the MapWindow is not refreshed with the Font changes performed through the Font Dialog.
The font size specified in the command dialog initially is used for conflict detection and creating the initial style of the output legend entry. The query editing permits only changes to the font size used in detecting conflicts and cannot have any effect on the legend entry(ies).
When the query is edited, all specified options( including font size) are honored and the number of conflicting and non-conflicting labels are calculated accordingly. Even in the Query Properties command dialog, the frame containing the Font button is classified as "Detection criteria" only.