I don't think that's true. You will still be able to do it with the nvram command line, which can use today in Yosemite (as well as previous OSX's) to set other nvram parameters.
Not saying it's ideal (it does still require a reboot), but it's better than having to reboot twice, including once in Recovery mode.
Having a TotalFinder that only works in rootless mode is better than not having a TF at all.
Barring that, having a Finder replacement (e.g. PathFinder'ish) is better than not having an integrated TF.
Thanks for TF. I really don't know why Apple refuses to do the "folders on top" thing.