Using Environment::get(), one can obtain variables not included in Environment::getAll(). This odd behavior is caused by EnvironmentVariable::getEnvironmentVariables() searching only $_ENV and $_SERVER, whereas EnvironmentVariable::getEnvironmentVariable() searches $_ENV, $_SERVER, and getenv().
I suggest including a call to getenv() inside of EnvironmentVariable::getEnvironmentVariables() for the purpose of pulling in any variables that may not be included in $_ENV (such as when variables_order is set to "GPCS" thus excluding $_ENV).
I am going to make this code change and submit a PR.