Studio One has basically 4 different independent timebases :
1. Transport primary timebase
2. Transport secondary timebase
3. Primary Ruler timebase
4. Secondary Ruler timebase.
Ctrl + T hotkey only works with whatever timebase is set in "Transport Primary Timebase". So in order for seconds timebase to show up in Goto Time command you need to set seconds timebase in Transport primary timebase.
Please read my feature request below to know more details. If you agree with what you read, consider upvoting it.
https://answers.presonus.com/76394/add-option-to-sync-ruler-timebase-to-transport-timebase