Yup, it's fine to update it yourself. Additionally, if you re-run the Autotune Configuration wizard, go to the FB App section and hit Refresh, it will grab the latest recommended settings for the Feb, March, and April changes that are upcoming. Then, just hit "Update Application" for the updates to be applied.
For all of them, it's correct to enable those migrations right now. JFBConnect is not adversely affected by any of them as we've made the changes required (where necessary) back in the v4.2 release.
You shouldn't see any difference once those migrations are enabled.
Hope that helps,
Alex