::I agree. Though not essential, the popup feature is nice and I didn't want to lose it through the choice of one or another other ref template family  apparently editors create templates with willy-nilly features that happen to occur to them, so maybe one has popups and another doesn't. But as you say it's so confused what's due to intended functionality vs. which browser vs. preference settings (logged in? IP?) vs. some random whoknowswhat that it's not a good investment of time to worry about it now. 
 ::I posted a query at WP:Village_pump_(technical)#Controlling_order_of_reflist but not much luck. Not sure I'm making clear to them (or even you) what I'm after so I'm going to mock something up. I've got the bit in my teeth now. 
 ::Side point: In converting parameterized cite templates to cite doi, I've noticed a non-obvious problem: often the old cite had a url to full text, but the doi cite gives url to the PMID entry instead (which in retrospect is not surprising) so the full-text url needs to be manually edited back into the doi template. I'll take care of these in this article but thought you should know for your work elsewhere.  
 ::