How do I set the options for a programatically created content type?
You can set a node_options_[type] variable,

e.g:

node_options_article: Array
(
    [0] =&gt; status
    [1] =&gt; promote
)


which can be set with:

// Make my_type nodes published and not promoted to front page by default
variable_set('node_options_my_type', array('status'));