Using the browser it should remember your settings, so if you turn PWA test off it should be off for each run. Unfortunately if your browser keeps resetting this there isn't much you can do in the developer tools version of Lighthouse.
However if you are willing to install the Google Lighthouse Command Line Interface (CLI) then you have full control and can automate the process.
I wrote about the benefits of using the Lighthouse CLI here.
To run Lighthouse without the PWA check you would run something similar to the following:
lighthouse https://yoursite.com --only-categories=performance,accessibility,best-practices,performance,seo --output html --output-path ./reports/not-a-pwa-report.html
The key part being --only-categories=
and then the tests you want to run.
The above example would output the HTML report to the specified path. All the options are listed on the linked Lighthouse page under CLI options.