Maybe try using a combination of Folder tracks, Group channels and Track Versions, and never put plug-in effects on the master outs, instead put plug-in effects only on the track inserts or on the Group channels. In this way, treat each bunch of tracks contained within each folder track as a ‘separate’ project within a project… to avoid having 100 different project files.
To manage such a project you could try using Visibility / Show Only Selected tracks (Right click in the Visibility tab of the Inspector).
RIP / Export might be better for this? Then you wouldn’t need to be timeline based, you could render as ‘separate events / complete signal path’ or ‘as one event’.