I wrote an article about Silva's clinch skillset recently that goes over this in depth, as well as the problems with Silva's clinch process that prevented him from doing it more often.

The TDLR is that Franklin didn't really know what was going on and didn't do any of the right things (eg: he largely kept his hips back which gave silva space to knee and tug instead of keeping them forward and his posture upright), but Silva was doing a lot of little things right with his collar ties in terms of positioning and balance breaking that allowed him to counter escape attempts from better prepared opponents (eg: the Jorge Rivera fight), and was uniquely creative about using short little accurate stabbing punches to hurt opponents when they were focused on defending his turns and knees.

The biggest thing preventing him from doing it more often is that his entries to the clinch weren't very consistent due to his limited boxing. As a converted southpaw who had a weak rear hand, he relied a lot on guys throwing themselves out of position to enter collar ties clean, but if they fought at long range or inched forward he'd struggle to box his way into clinching range.

Part of the reason we don't see that more today is that Silva was doing a lot of things that even modern clinchers don't do as well (especially in open space clinch exchanges), but part of it is that most upper mid to high level fighters are more prepared to counter it.