I think you might be making things a little bit more difficult than they need to be. This seems to stem from your use of what might be a few too many tools, but you may also be missing a key piece of what makes Bootstrap so attractive.
Bootstrap has a very particular vocabulary that's used to describe its assets, a vocabulary which is reflected in its css styles. Panels, wells, buttons, notifications, icons-- all should come well-documented in your theme demo and are usually very consistent with other Bootstrap theme naming conventions.
This is what your Dev is talking about when he talks about using assets from the theme. Even though you may use PS to approximate a theme, you should still be basing your mockups on the look and feel of the theme assets. Gather the name of those assets from your demo and CSS documents before starting layout work, and make notes of the assets you use as you go along.
I'd also question the need to go from PS to IV to PS to Zeplin. Likely you can manage all of your work in PS for non-interactive mockups, and IV when you need to manage workflows and collaboration.
I hope that helps! Let me know if you have any questions.