Under "Insert Reference" > "Workflow Variables" only some are shown and I cannot figure out why these are shown and others not.
usually you should be able to find the variables you need. There are some cases however, that certain variables don't make send. For example: You can't use a variable of type number as a recipient of a mail. Thus you won't be able to pick number variables in recipient field.
To be more precise it would be helpful to have an example what type of variable you want to use in which scenario.