Tbh, I'm not 100% sure about Suguha. There might have been some agreement in the early stages of Part 2, but I don't remember all the choices and dialogue. But I think it's because he allowed her to test her time-stop ability on him, that I know for sure. As for the others, Inoda has permission for Asuna since Part 1, given by Kirito when he saved her from the bandits (which is strange, tbh, that a third person can give such permission). As for Sinon, it was Kirito's choice to allow it. To be fair, these small details that Fujino likes to add between the lines are not easy to grasp in the bigger picture and aren't always plausible or convenient, so it's easy to miss.