What happens if the is scratch is deep enough to catch your fingernail + autogeek + autogeek

As the title says, What happens if your scratches are deep enough to catch your fingernail? What then? What are my options? I recenly purchased an Acura TSX 2010 and noticed there are 2 paint chips on my hood that are rusty (see attached). After see Larry Kosilla's video, YouTube I have decided to get my mechanic to use touch up paint (since I know nothing about detailing although I'm learning a lot here ;)) and use the Loew Cornell Fine Line Painting Pen. My car has Grigio Metallic paint and I'm looking ways to make my paint POP and get that WET look.

If my chip is deep will it take multiple attempts to get it to leveled off? Will Loew's not work because it is more for small rock chips? Maybe I should ask my mechanic to use Dr. Color Chip instead? UGH! :confused::mad::dunno:

BTW has anyone used the Loew Cornell Fine Line Painting Pen? Can you tell me your pros and cons to Loew Cornell Painting Pen compared to Dr. Color Chip? From what I see Larry do in the video it seems a more precise instrument and as it seems NOT to leave a BLOB on the paint. TIA