Beginning in v39 Beta 2, we added support to Logos to open ref.ly links directly without opening a browser tab. To do that, we registered Logos in Windows' "Apps for websites" function, which is Microsoft's recommended approach for tools to directly open links that would otherwise go to your web browser. Unfortunately, a small number of apps do not support Apps for websites, including Microsoft's own Office suite. We understand that users frequently use Office alongside Logos and wish that Office supported Apps for websites.
If you would like to express similar disappointment, you can provide feedback to Microsoft directly in the Office apps through the in-app feedback function. One example of a helpful message might look like this:
I have installed Logos Bible Study. It has an "Apps for websites" handler for ref.ly that is enabled in Window Settings (under Apps > Apps for websites). When I enter the URL https://ref.ly/Jn3:16 into Wordpad and click it, it opens the associated "App for website". However, when I enter that URL into Word and click it, it opens my default browser. Word should respect the "Apps for websites" that are configured in Windows.
In the meantime, we have found a method to work around the limitations in Microsoft Office. The registry script found here should redirect links from Office to properly respect Apps for websites. All other links should open in your preferred browser as expected. This script has been tested on Chrome, Firefox, Edge, Edge (Dev), Brave and Opera.
Opening ref.ly links in Microsoft Office on Mac is unaffected and should open directly into Logos.