IMO a few things are need to be resolved for this to progress:
1. As @AdamDanischewski said, some UI control is needed. The prefect solution IMO is to extend the keybindings UI to allow binding to mouse buttons (with modifiers) as well, so called "clickbindings".
Some mice have many buttons and these could be bound by the user to suit their use-case, while other users may keep the current ctrl-click and bind the multiple select elsewhere and others go for interapp compatibility. Giving the user control takes the heat out of the debate about backward compatibility vs interapp commonality.
This would need a bit of work because the current keybindings are based on `gtk_accellerator` which does not handle clicks IIUC, but I think its just MMOP to have the click handler use bindings instead of being hard coded and to store and retrieve click to action mappings, eg in `clickbindings.conf` like `keybindings.conf`.
2. A plan is needed to introduce multiple select into Geany. As has been said elsewhere, none of Geany is written to support multiple selects. It would be my recommendation that multiple selects be introduced progressively instead of as one big lump. In practice the project does poorly with big lumps because it doesn't have the effort available to review and test them.
But before _any_ multiple select capability is introduced it must be checked that _no_ other Geany and core plugin functionality is affected by their presence and any problems fixed.
Then the basic ability to make multiple selections and type in them, as @Ryan1729 has here, can be added and contributions solicited for making other Geany functions multiple select aware when it makes sense for that.
3. The ability to style the secondary selections can be added, Scintilla can do it, so the settings "just" need to be added to Geany and appropriate colour schemes.