What is the correct way to programatically set node type options?
Looking at the code for node_type_form_submit you can see that the variables are set before the node_type_save() function is called. Thinking about it a bit, it doesn't really matter as the node type info is saved into a different table than variables. So as long as the variables are being set synchronously with the creation of the node type, it shouldn't matter. Even then, the worst case scenario would be you'll have some redundant variables in the variables table. Which is not a big issue.

So to answer the question, yes that's the proper way. However I'd do it in the same function call in the .install file, maybe implement it in hook_install or hook_enable depending on what you need.