It is possible to force them to be exactly where you want them —
t = linspace(0, 5, 500);
x = cos(2*pi*t);
y = sin(2*pi*t);
figure
plot3(x, y, t)
xt = xticks;
yt = yticks;
text(median(xt),min(yt)-0.5, 0, sprintf('x'), 'Horiz','center', 'Vert','middle')
text(min(xt)-0.5,median(yt), 0, sprintf('y'), 'Horiz','center', 'Vert','middle')
grid on
% view(0,90) % Top-Down View (Optional)
They are in the centres of their respective axes here, although it is necessary to rotate the plot to see that, since the perspective distorts their positions.
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