Hi Zac,
Thanks for posting in the community. We are happy to help you.
I have tested it on my end and can reproduce the same situation. Based on my research, currently, there is no built-in setting/feature that can change this behavior. In this case, if you want to create a loop page by the template in the same workspace, you can duplicate the subpages and drag them under the newly created master page.
I understand the inconvenience that happened to you. Since Microsoft Loop is a relatively new tool, and its features are still evolving, I recommend you vote for the following suggestions in our Microsoft Feedback Portal where other members also post and vote for their suggestions. It's the platform for us to hear your voice and improve our product.
Save page as template must include the Subpages
Duplicate a page that contains subpages
Sorry for the inconvenience that you experienced. Appreciate your understanding and patience.
Sincerely,
George | Microsoft Community Moderator