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Well, both HoT and PoF final fights weren't turned in a strike so it doesn't really mean much.
Also where did they say they the strikes will be part of the story of the first 2 maps?
Of course it can't spoil anything from the third map, but it could also be a rift enemy, for example. Or a meta boss like the boneskinner
Especially for the first map, we could have no big boss at all during the story
I am assuming they will do the same they did in EOD maps - strikes were included in the story, that's how they save resources by reusing those fights. Dragons end was reused two times, in meta, story and in strike. I don't think they will stop doing that. It would make sense to be rift enemy, considering they said they will introduce one more tier of rifts later. That's a good idea. Well we won't have to wait long to find out either way
Current fractal is technically part of story (elaborates more in story). So even if we assume strikes r directly from story instance, fractal is still relevant to story (current form). I personally don't have expectation one way or other, i'll just wait to see what they release on that front.