Is it ok to have methods such as tasks and global variables that are created outside of the basic template?

If you're asking if it is possible to use your own tasks, functions, and global variables and still be compliant with the template, then the answer is yes.
Remember that the template is just to standardize the interaction with the FMS/FCS for all teams. As long as you do not break that portion of it, you should be good. You do not have to squeeze all your code into the main task and initialize function provided by the template.