Yeah, not only the secret ending gets added, but sidequests that interfere in some ways with the main quest line. Please don't quote or paraphrase the following sentences, more experienced Skyrim mod authors and actual programmers (think of people like Arthmoor, DavidJCobb, Mator etc.) can probably put it in better words.
The creation engine is known for putting a lot of stuff in your save games e.g. script properties and such. It's pretty risky to change these values around during a playthrough.
Let me give a simple example of what I mean: We changed these values here and there in a couple of our patches with the sidenote: "This only works for new saves, where feature xyz is not enabled yet.", e.g. think of the patch where we moved the fast travel marker for the South Quarters closer to the myrad tower to shorten the overall travel time etc. - this worked for new save games, in which the player neither entered the South Quarters nor enabled the fast traveling system in Ark while entering through the front gate with Jespar. But old save games saved the old position of the fast travel marker in the South Quarter, since the script and the reference of the marker were already initialized, hence the player still got teleported to the old marker instead to the new position / the player wasn't teleported at all.
And this happens in a much larger aspect when FS is released. So stopping a playthrough, to wait for FS is not really worth it - even if you only have little time to play games - it's simply not worth the risk to run into "newly added bugs" because the engine can't handle certain changes that well. We put a lot of thought into having so called Failsafes in case people install FS mid playthrough, but some stuff just can't be thought of or is way to complex e.g. the new class "The Phasmalist" which is probably more complex than the other skill trees combined. We have a couple of testers right now, but they all test with new save games (= started completely new playthroughs).
tl;dr
Starting a new playthrough is heavily recommended. We don't have the time and man power to make sure that Forgotten Stories works with all its features when it is installed mid playthrough. Though, we try our very best.
Edit: Wording