Status Bar Padding - Go to Personalize > Themes > Status Bar & Scroll Down - From there, set the first thing to default then: Left & Right Padding to "2/4px"
Refresh Rate is Stuck @90hz even when turned off Smooth Display - Enable Developer Options - Scroll down and Disable anything related to Refresh Rate (eg. Force Peak Refresh Rate)
MTP/USB options not available to be changed - Enable Developer Options and check from there - or System > USB Configuration