Yes, you can enable it in your the LibreWolf specific UI or in your overrides. There aren't significant downsides as Firefox Sync encrypts your data locally before transmitting it to the server. Additionally, you can self-host the old version of the server if you really don't want to use Mozilla's, and there's work being done to have the new version equally easy to self-host. Find out more about the technical details of Sync's implementation here and here.
When using Sync across multiple installations you might want to disable settings synchronization to avoid unintentional changes.
Haven't tried it, but I'm guessing if you log on to sync on FF, it potentially might interfere with LW's configuration when it tries to sync? I'm curious as well and hopefully someone can give you a definitive answer.