No, you don't have to.
1. Just start version 59, create your setting there like what you always do before.
2. Exit the program, copy the cache folder from version 59 folder to version 63 or 65 folder. Just use drag and drop. If it ask you to overwrite, go do it.
3. Run version 63 and 65. You will see that all your settings are imported there and converted to logic rules . If you set a certain pokemon as favorite and you chose "protect favorite" from previous version, that pokemon will only have "catch" and no transfer or evolve on logic rules.
4. Further customize it to your desire. I set kakuna and metapod to zero, for example.
For now, I'm still using version 59. Niantic hasn't forced updated yet, so API 49 is still perfectly safe. Looting pokestop when bag is full is buggy, but I found a way around it. I will switch to version 63 once Niantic forced the update to API 51. But if you are looking for a fast way to set the logic rules, that's the fastest way, instead of doing it one at a time.