Here's how I see the knightmare/flash thing:
1. The two things are related. The apocolyptic future is an Injustice nod; Lois' death (it's clearly Lois that has died--not Martha) has made Supes totally evil, with his own army of fascist brutes; Bats has his own faction of rebels. After waking up from that vision/dream (or temporal displacement from Flash?) Bruce is faced with the portal, containing Flash and his warning. The warning is about finding the other metas to stop Supes when/if he goes rogue, and prevent this future.
If this is correct, then my questions are these: what is Darkseid's role in this? It seems like Supes is just evil due to his loss, not under DS' control. Are they working together? Or has Supes' evilness let DS win, but he and Supes are still enemies (of each other and of Bats and co.)?
2. The two things are not related. The knightmare is simply a dream/vision of a future where the 1% chance of rogue Supes has happened. It is fueled by Bruce's fear and paranoia. He wakes up from the dream/vision, and sees Flash, come from a DIFFERENT future to deliver a warning about some other threat which the JL needs to form to combat.
If this is correct, my questions are these:
1. Who is the "he" Bruce was right about? Is it Supes? Is it Darkseid? Lex?
2. What is Lois the key to? It would seem weird, if Lois' death causes Supes' heel turn, to refer to Lois as "the key." it would make more sense to say "save Lois." or "protect Lois"
So what is she the key to? Finding the metas? Getting Bruce to save Martha (THAT future with Martha dead could be the future flash is from, not the Knightmare one)?