Hey I'm the OP on my own minecraft server and for some reason I keep getting the message "[VNP] Opening chest silently. Can not edit." Whenever I try to open a protected chest. Yes, I know that it's due to the vanish.silentchests permission node, but I don't want that limitation for myself. But OP has every permission by default. How can I still be OP and not have that particular permission restricting me?

OP does not have every node by default. Read the documentation for VNP. My guess is you have the * node, which IS saying "I want every node ever"