The gift Eveline gave Margarete wasn't supposed to be the serum ingredients, I don't think. I thought it was the name the Bakers had given the infecton. As far as the serum ingredients the way I understand it is that Lucas had received them from Tentsu, the organization behind Eveline, to synthesize his own serum (he isn't controlled by Eveline in the game), and I assumed he had hid them around. But I'm not sure.
I don't think the game explains why the boat situation occured, but I believe the implication was that she disliked Alan (Alan says "that bitch never liked me", or something like that) and attacked him. Weak, I know.
Umbrella seems to have been scouting the Bakers for awhile. I believe their are photos the Bakers (maybe Zoe) took of the helicopter, so they might have been keeping an eye on them for awhile and only intervined when the situation exploded.
I'd disagree, especially when it's called 'Resident Evil 7'.
Up until the Chris cameo, and a few easter eggs, Resident Evil 7 could have been a really good Resident Evil inspired indie game. Narrative ties are a big part of feeling like part of a franchise, especially as gameplay is prone to change. The only franchise exempt from that is Final Fantasy, I think.