Actually, bulkheads are designed to not use silicone or teflon tape. You should use/need neither. Just make sure the gasket is seated properly on the flange side of the bulkhead. The gasket should be doing all the work.
If the inside of the bulkhead is threaded, then sure, add teflon tape to the MPT fitting you will be screwing in. Otherwise, the bulkhead itself requires nothing.
You can see by the diagram that if water is unable to seep past the gasket, then the threads will be dry. So teflon tape isn't necessary. Also, too much teflon tape is bad. Its supposed to seal the threads, not interfere with them.
I use silicone on the 'dry' side of the tank because I drilled sub-standard holes. (i.e. the drill bit slipped a bit and scratched the glass, as well as having the glass chip on the 'wet' side.)
The bulkhead does do its job, provided you did yours.
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