Applying for Masters Program at University I work at as a Developer
That depends on the university and its rules. General advice is probably worthless. It may be more lenient for an MS than a doctorate, perhaps. But the competition will still be there, and there may be specific rules about candidate selection.
I would expect that most places tuition reimbursement is a complete separate issue than placement into a program.
My advice, if you want an MS is to apply to more than one university. Include this one, of course, but don't cast a small net.