Steve is spot on
I am sure she will be fine. I have not had a queen superseded after marking and I have occasionally masonary painted one. I have a bit of a love hate relationship with Posca’s. The fact we may use them so infrequently and being stored for months between uses can’t help much, but the sticking out or in nib issue does make getting them working on a hive part first highly recommended.
Personally I use a crown of thorns cage or one of the plunger types to hold the Queen static for a few moments. I may have misunderstood you but the queen clip is not really suitable as she is too mobile - I don’t actually use mine ever, I think they are potentially lethal. The upside of the thorns cage is you never need to handle the queen and she is static but she is on a frame and typically workers take an interest and mob the cage top getting in the way and even trying to clean off the mark. I usually catch the queen securely and then take the frame a few feet away to reduce traffic. A puff of my fetid breath may clear them as well. Same with a plunger held queen, though in that case I pick her up first to pop into the tube before inserting the foam plunger as chasing her around to try to get her to walk up into it is not restful for me or her. Queens can quite quickly become skittish if hassled too long and that’s when mistakes happen.
Whether marking or clipping (and I generally do them on different occasions) there is benefit in just getting on with it. If it is turning into a bit of a saga, leave it for next time and let everyone calm down again. Knowing you are going to mark, get your pen working then put your pen and cage within arms length on a neighbouring hive roof. That way, when you find the queen on the right frame, you can keep her in sight, move the frame towards your kit and pick up your cage using peripheral vision to locate it, then pop it over her when she is positioned appropriately. If you leave it in your bee box or pocket, by the time you have glanced away to get it out, even though you
know she has to still be on that frame somewhere, she will have inexplicably slipped through a portal in time and space disappearing entirely....