Make sure that nothing arbitrarily limits your fps, like VSync or the Force Fps in the project settings.
When you see that Godot is using 60% of your CPU, it doesn't mean that it is not using it as much as it could. Your CPU is made of multiple cores, and any program can only use so many at once. If you want Godot to better share the work among your different CPU cores, you can try to set Rendering/Threads/Thread Model to Multi-Threaded.
Also, if you manage to isolate a specific task that takes a lot of time, you can put it on its own Thread. Threads do not necessarily run on different cores from one another, but you are explicitly telling your operating system that it may do so.
Finally, there can be various bottlenecks. If the program is waiting for your storage, the system runs low on RAM, etc, then you will see big slowdowns, even if your program seems idle CPU-wise.