1) No, the cix file will not work with the AMD loader. A CIX file is used to describe a visible namespace, e.g. "dojo.byId", providing the signature and documentation.
2) The dojo cix generator is quite old, so the dojo documentation format may have changed, as well as the methodology (i.e. AMD loader). Normally you can use a JSDoc comment to override what the type information Komodo thinks it is:
define(['dojo/dom-construct'], function(cons){
/** @type String */
var lcons = cons;
lcons
});