As a stopgap you can consider opening whitespace - I like my queries aligned, with the city 3 spaces from SELECT, which would align with FROM etc... Opening whitespace is kept even when trailing is dropped.
Obviously not a solution, but perhaps a workaround?
In Project Options > Code Editing, there's a Strip trailing horizontal whitespace when saving setting that caused the issue. That setting is under Global Options too, Global Options > Code > Saving, and it is not selected. When I create a new project via usethis::create_project(), the global option is ignored and it is selected in the new project.