It depends on the particular racial substitution level,

In general they are a variant of normal classes that only members of certain race can take. They usually trade stuff for stuff, to continue with the Elven wizard substitution level, you trade the ability to specialize for extra spell known and an extra spell slot.

They also can modify stuff such as HD (from memory Dwarf fighters get d12 instead of d10) skill set (Elven wizards add search to their skill set) or even skill points per level (changeling rogues get 10 +int skill points per level); but these changes only apply on said level, does it makes sense?