The striker can be at full cock,,wether the Safety is ON (full forward) or OFF (full back).
If it is cocked,,the cocking indicator will be showing at top the frame. The earlier style cocking indicator was on the bolt top surface itself.
But worked the same way. Rifle cocked,,it protrudes,,uncocked,,it's down flush with the surface.

The 1899/99 Safety simply blocks the trigger from pivoting and locks the lever from opening. It does nothing more.

What position the Safety is in makes no difference as to wether the rifle mechanism is in the Cocked or Uncocked state once the lever is closed, breech locked shut.

The cocking indicator works directy off of the striker, Nothing to do with the Safety position.

With the striker at the cocked position you can move the Safety back and forth betw the Safe an Fire positions all you want,,the striker will remain at full cock.
That has no effect on the striker, the indicator will remain exposed. The striker is totally independent of the Safety. Manipulating the Safety to Off does not lower the striker to a 'half cock' or other 'safety state' and then back to full cock when the Safety is re-engaged to the Fire position..


You do have to have the Safety in the rear position (Off/Fire) in order for the lever to be able to close all the way and lock the breech shut if that is the worry.
If the Safety is in the forward (On/Safe) position it blocks the lever from closing the last little way
But that is something that occures naturally in the operation of the rifle. I can't think of an instance where the shooter would re=engage the Safety to the forward position between shots (lever open) and then try to close the action.
It's just not a natural sequence of firing events to any manual operated firearm.