I don’t think it’s a bug but more so a missing feature/consideration.
The expected behavior from those coming from Photoshop is that the Activate Line Tool action should only work when the Freehand Brush Tool is currently selected, not when you’re using a different tool like the Freehand Selection Tool. Krita however doesn’t have a conditional for what tool you’re currently using so the Activate Line Tool always triggers and can block the modifier keys from being applied to the current tool like Shift + Left Click.
This functionality can’t work as a plugin because plugins can’t override canvas input actions but you can get it to work in your own build of Krita by editing kis_tool_invocation_action.cpp
Before:
After:
This feature is possible and should be implemented as a default for Krita.