You can't set the plot size in absolute terms with tiledlayout. You would have to layout the axes positions explicitly, e.g.,
% Position in normalized units: [left bottom width height]
ax1 = axes('Position', [0.1 0.6 0.3 0.3]);
plot(ax1, rand(10,1));
ax2 = axes('Position', [0.5 0.6 0.3 0.3]);
plot(ax2, rand(10,1));
One option though might be to use the same tile grid dimensions in all figures, but put dummy, hidden plots in the unused tiles, e.g.,
figure;
tl=tiledlayout(1,4);
for i=1:4, nexttile; plot(rand(1,5)); axis square; end
figure;
tl=tiledlayout(1,4);
for i=1:4,
ax=nexttile;
plot(rand(1,5)); axis square;
if ~ismember(i,[2,3]),
set([ax,ax.Children],Visible='off');
end
end
