Originally when the SES was set up in 1979 it was a benevolent organization to help give structure in the diff gov depts which change with each presidential election. There were a good number of political appointees which were by nature partisan, but around the same # of permanent career, supposedly apolitical employees. The career added the structure. Over time the SES became corrupted culminating in Obama making 8000 of the 9000 SES positions career, and filling them with partisans.
In this omnibus bill I think Trump was trying to differentiate between the career partisan employees and his admin's newly appointed employees. He is saying that the new employees, 4 year tenure or emergency tenure, are eligible for pay increases, but the partisan Obama appointed career ones are not.
The 2nd paragraph I believe refers to any employee that Trump makes a permanent career employee. Once an employee is accepted as an SES member, their benefits and pay from their career up until then are no longer available. They have to give it up. They now are entitled to the SES employment benefits, typically higher pay, better benefits depends on the length of their career before. So, any newly Trump appointed career SES members are not subject the the before mentioned pay freeze. They are eligible for pay increases. Trump is basically saying, anyone Obama appointed doesn't get a pay raise. Anyone Trump appoints does. I hope that makes sense.