On the "Create a new scratch org" page -- since SFDC recommends that Scratch Org definition files go in VCS (see https://developer.salesforce.com/docs/atlas.en-us.sfdx_dev.meta/sfdx_dev/sfdx_dev_scratch_orgs_def_file.htm)

then the Upload dialog should offer an option to browse repo/branch/folder for the desired Scratch Org Definition file (default path would be main/config)

and, once selected, the other portions of the page that are overridden by the Scratch Org definition file should be both populated and disabled so the user gets a confirmatory echoing of choosing the right scratch org definition file