Customizing Search Result Display for .eml files at Site Collection level

You may want to consider the following options:
a. Rerun the migration and ensure the filename contains the subject
Note: using the subject in emails from a thread is not very useful since you may end up <subject> (1), <subject> (2). It would be better to capture the subject with another email field like sent date to make the name unique. There are many tools that offer this functionality as Outlook add-in or as SharePoint app.
b. PowerShell (providing this is feasible as SCA in your tenant)
c. Use Power Automate
d. Use tools offering the capability to use the email subject to rename emails stored in SharePoint (e.g., https://www.slimapplications.com/product/bulkmetadatamanager).

The above example uses a clientID/secretID generated a site collection level. If you can access the URL https://<tenant>.sharepoint.com/sites/<sitename>/_layouts/15/AppRegNew.aspx this should work without requiring access to the SharePoint tenant or Entra ID.

The root of the problem is the limited functionality SharePoint offers for managing emails. This is the reason there are many 3rd party apps to address this functionality gap.