If you're getting a PowerShell message about turning on developer mode, it's because you're running a script to do so. This is likely the Add-AppDevPackage.ps1 script that Visual Studio generates when creating an appx. That script shouldn't be used for production. It is designed for development / test deployments, and two of the three things it adds to the install are turning on developer mode and trusting your test certificate. Neither of these are needed or appropriate for production.
For production deployment with Intune, you (or more likely, your IT team) will need to sign the app with a trusted certificate and then deploy the MSIX and its dependencies. See Distribute your MSIX in an enterprise environment - Microsoft Intune.
If you need more help on configuring Intune, you'll probably need to post a question specifically about that under the appropriate Intune tag.