The idea is that pharma is perfectly, 100% sterile after terminal sterilization. Any compromise of the vial could introduce bacteria that could, over time multiply to the point of causing an infection. They don't want a vial pierced and reused months later.
Sterile filtration isn't 100% effective. As a practical matter what really protects against a vial becoming overrun with bacteria is the bacteriostatic environment created by benzyl alcohol. Just use proper aseptic technique. Sterilize the stopper, use a sterile syringe, and the amount of bacteria you'd introduce into a new sterile vial is inconsequential and not going to overcome the bacteriostatic environment, A good quality stopper fully heals, but to be extra certain, there's a sterile vial sealing sticker you can use to ensure the stopper is fully sealed.