Strats tend to run closer to the edge of the fretboard, depending on the nut and bridge.
A change at the nut will effect things at the nut end more... and have almost no effect at the bridge end of things. The reverse is true.
The thing to check - is how even is the spacing of the strings and, are the two E's centered edge to edge.
Of all the Warmoth bodies and necks I've assembled (5... 6?.. something like that), I've never had an alignment issue that was NOT the cause of a tight neck pocket and some finish buildup altering things just a wee wee bit. That is, if I could pull the neck into alignment with the screws a bit loosened, I knew it was a simple matter of some pocket cleanup to get it 100 percent perfect. Neck pockets should NOT be super tight, but just a bit of an almost no tolorance drop in. Fender factory necks are relatively loose in the pockets compared to Warmoth, and they do just fine. You might need to check for finish buildup and or an overhanging pickguard, or swelled laminate, or ... just needing a bit of easing. You will have to remove almost no material at all. Go super slow - sanding not filing. Use a block (you'll need to make your own). A very few minutes with some 320 grit paper and all of my necks were dead center, and still relatively tight (much tighter than Fender factory necks).
Also remember, what you remove from the bottom side of one edge, also gets removed from the top opposite side. That is, if the neck must be "rotated" a bit counter clockwise to get more edge space, you'd want to sand the bottom right and upper left sides of the pocket - just a little bit, to clean them up.