It's scored by round. 5 rounds total. Santos clearly won the 1,2, and 5th rounds. Jones did next to nothing in those rounds and did almost all of his damage in the 3 and 4th rounds. A few of his shots were flush but overall Santos landed more flush shots. Some of Jones' shots were glancing at best and Santos fell a few times simply because his knee was unstable.
Go back and watch the 1,2, and 5th rounds individually and explain how a single one of those 3 could have been for Jones. I did it twice last night on catch up replay and Jones wasn't really close in any of those rounds. Since neither fighter came close to a 10-8 round that makes it clearly 48-47 Santos.
The judges might be picked by the commission but they know how powerful the promotion is in getting them work and if they want to keep getting work then giving a judgement against the golden boy who the promotion will actually relocate an event venue last second for would be a bad thing for their future. Just like boxing. It's corrupt.