I went through this when I was younger and then I realized how it caused problems trying to organize by "story" or by "crossover" or theme.
Alphabetically by publisher and then just go in and pull out what you want to read when you want to read it.
I'm laughing at the "situation" not anyone's filing system. I've got about a 60 longbox collection organized this way and it's the only real way to go. Just keep titles by titles. Also, one-shots and mini-series typically file by I.P. alphabetically anyway - a Batman mini for example normally starts with "Batman: Mini- XYZ" and the few exceptions that don't can still just go in alphabetically by title.
Also, like you I keep spreadsheets on my "inventory" and "collection". It's been an evolving monster for 20 years and for the last many years I just did the same thing as the boxes..... Tabs for each publisher, alphabetically. And when you need to find something quickly or you forget an entire title you can search by "Ctrl-F" and jump right to where you want to go.
I love this stuff - been doing it for decades now, which sounds crazy considering I'm still under 45 years old. I keep master sheets of costs and quantities as well. They self-compute when I add books to the inventory. It helps me run the metrics of what this monster hobby has cost me over the years.
I suppose the "bundle it by story and crossover" thing can work when you have a somewhat small collection. But take the Superman "diamond" numbering system from back in the day as an example. Instead of filing "Action Comics # whatever (1991 Diamond number 1) and then putting "Superman the Man of Steel # whatever (1991 Diamond Number 2) after it, it's still better to just file Action comics with Action Comics and Superman the Man of Steel with Superman the Man of Steel.