Yes, events will synchronize with every command submitted before the signal and after the wait, provided that they match the pipeline stage. If you really want maximum independence here, you'd need to submit these sets of commands to different queues/queue families.

However, you should also keep in mind that just because the driver could schedule work in parallel, it doesn't necessarily do so - this depends on the size of your submissions and free hardware resources. Using multiple queues also isn't free, so you should benchmark whether that split is really worth it.