If you haven't called hold on (or otherwise set the 'NextPlot' axes property, which is what hold does), then plot() does other things besides just creating a line (or lines) in an axes, including setting the axes x- and y-limits, deleting existing lines from the axes, and (apparently) setting the XAxisLocation and YAxisLocation. As you point out, using hold(ax1, "on") before the plot command avoids changing those settings. So that's the answer to your first question (Why does plot reset the axes?): plot() without hold on does other stuff.
To answer your second question (Is hold on really necessary?) Not if you don't use plot() at all. In a situation where you set up your axes before creating any lines, it's probably more convenient to use line() instead of plot(). line() is a low-level function that just creates a line and doesn't change any axes properties. (line() doesn't allow the same set of input arguments that plot() allows for specifying line properties, so you have to set them using property/value pairs.)
fig1 = figure(1);
ax1 = axes("Parent",fig1);
axis(ax1, [-1 1 -1 1]);
ax1.XAxisLocation = "origin";
ax1.YAxisLocation = "origin";
x = [-1,2,3,4];
y = x.*2;
line(ax1,x,y,"Color","r","LineStyle","-","Marker","x")
