Subalgebras whose root system is not a subset of the root system of the original algebra are called special subalgebras. Therefore, the generators are not a subset of the original's group generators.
That is not quite right. A special subalgebra is one such that their step operators do not form a subset of the algebra step operators.That is what is meant by a root system not being a subset of another root system. It does not imply that the subalgebra generators are not a subset of the algebra generators.
Example: Consider the three dimensional representation of g=su(3), whose generators Ta=λa/2, where λa are the Gell-Mann matrices. The step operators are
E±α1=T1±iT2,E±α2=T6±iT7,E±(α1+α2)=T4±iT5,
Regular embedding: The generators T1, T2 and T3 form a subalgebra su(2). This subalgebra step operators are t±=T1±iT2=E±α1. The subalgebra step operators form a subset of the algebra step operators.
Special embedding: Another su(2) subalgebra is given by T2, T5 and T7. In this case the step operators are t±=T5±iT7 which cannot be written as a subset of the step operators of su(3).
Notice the branching rules for the first embedding is 3=2⊕1 while for the second is 3=3.