I submitted a fix so dojo.require() are execute before dojo actually starts to parse the partial html. This is *not* due to the JS aggregator at all, it fails with it selected or not. This also helped me discover a bug in dojo that I submitted to the dojo team :-)
Now, you can fix your issue y simply loading extlib.dijit.Tooltip at the page level. Even if the fix above solves the problem, I will still advise you to do it so the module will be part of the aggregated js file. Else, it will be loaded lately using regular dojo loading mechanism.