Glossary Restyling Script creating htm files for each glossary term instance

We're using Robohelp HTML 11 and Robohelp's Glossary functionality is severely limited. We need our glossary hotspots to be pop-ups, so we use the Output Generator with Glossary Restyling Script, but when we use the pop-up option, it creates an additional html file for each instance of a glossary term instead of mapping all references to a single file for a glossary term. Why does it do this? And is there a way to fix it? The tooltip option does not do this, but it isn't smart enough to keep the pop-ups from going off screen. The additional 10,000 to 11,000 files that this creates is a problem for us, as each file has to be installed individually with our software.

While we're on the subject, is there a way to tell Robohelp to unmark Glossary hotspots? Or to avoid certain styles like headings or special text where we do not want to have glossary hotspots? We had to have someone write a script to fix these issues, but it seems like this should be a standard function.