NppExec (ver. 0.3 RC1 or higher) allows you to create and modify (heritable) environment variables using NppExec's commands "env_set" and "env_unset". See NppExec's help [3.1] for more details about the commands "env_set" and "env_unset".
Consider such heritable environment variables as "real" environment variables: these variables exist both inside NppExec (in a form of $(SYS.<var>) which allows you to use the var's value inside NppExec) and outside NppExec (usually in a form of %<var>% which allows to use and modify the var's value inside external tool).
NppExec allows to modify and restore a value of such existing environment variable, and to create, modify and remove such new environment variable (which did not exist before you create it in NppExec).
See also: Environment [4.2].