You would need to use i and/or j, depending on how you are thinking of an "iteration" for your algorithm, as indices into your data.idx# fields. If i and/or j are large, I would also recommend pre-allocating them as a logical/boolean vector/matrix, as appropriate for your definition of iteration.
For example, it seems like you would want to store all combinations of i and j, based on your code so you might do something like this:
L = length(fieldnames(data));
data.idx2 = zeros(L-1, L-1, 'logical');
data.idx3 = data.idx2;
data.idx4 = data.idx2;
for j = 2:L
for i = 1:L-1
firstoutput = data.(sprintf("variables_%d", i));
secondoutput = data.(sprintf("variables_%d",j));
data.idx2(i,j) = ismember(firstoutput(:,2),secondoutput(:,2));
data.idx3(i,j) = ismember(firstoutput(:,3),secondoutput(:,3));
data.idx4(i,j) = ismember(firstoutput(:,4),secondoutput(:,4));
end
end
