Tested in MicroStation CONNECT 10.17.00.209
At one time I thought you could prevent a variable from being set in a later config by undefining it, then locking it.
%undef VARIABLE %lock VARIABLE
But when I actually tried this with the MS_DISALLOWRELATIVEREFPATH variable it didn't work, as a test I tried:
%undef MS_DISALLOWRELATIVEREFPATH %lock MS_DISALLOWRELATIVEREFPATH MS_DISALLOWRELATIVEREFPATH = 1
And the variable was still being set.