The function has been implemented in designer in order to make deployments of whole projects through test and productions stages more easy and more consistent. A solution developer can within a single action reliably move the whole modelling solution (i.e., project) from one test system to a production system.
We are also aware that in some cases modeler may want to deploy just schema and associated sub-models (roles, custom actions, scripts) and for this reason, designer asks whether to deploy models as well.
For cases where modeler misclicks and deploys unwanted models to Model In-Tray (or for general cases where In-Tray ends up with lots of unwanted models), it is possible to remove models from In-Tray one by one, or to empty the whole In-Tray with a single action: