If you want to adjust tracker, you don't need to set keyframes on first frame if you already successfully tracked part of shot. Find the last good frame, delete forward (or backward if doing reverse) track that is off, adjust pattern or search region and track on from that point. There are buttons in tracker ui for both deleting part of track forward or backward from current frame and for removing keyframes. Tracker falls off for two reasons only: searchable pattern is outside of search region or it doesn't find match below error threshold (which is in the end the reason in first case too). If you delete forward track that is off and step to next frame, you see how far the pattern jumps. This gives an idea of necessary search region size. Capturing new pattern is necessary when match error goes above set threshold, usually due to pattern change from perspective etc or due to lighting changes. Changing pattern on first frame and retracking from start when tracker slips at frame 200 or something is kind of useless, because what you actually want is to capture is new pattern, not just different crop of old one.
By connecting something to A2 input of Merge node it does not "know to use it for alpha". It is used as just that, an A2 input, which is producing the cascade of A2 over A1 over B. Only because mix is set to low value it kind of works. Drive mix to 1.0 and it is pretty clear it does not mask and A2 input is not used as masking alpha. There is a mask input on most nodes to apply actual mask.
For moving the center of transform there is a very easy way: hold Ctrl and drag it with left mouse button where you want it.
PS. Right and up node layout is really strange to watch, no-one does that in Nuke...