They will convert to academy status
You are correct that VA schools that convert to academy status can keep their existing admissions policy. An independent school converting to a free school is also not subject to the 50% cap. This has not stopped the Catholic church preventing St Mary's College, Crosby converting from an independent school to a free school.
Note that the Catholic church has recently toughened its policy on this. There are two Catholic free schools in existence, set up prior to the change.
So you may be correct that these schools will become academies. However, given events in Crosby, I would not be certain about that until it happens.