writematrix() does not support any ways to configure the end of line.
However, if the issue issue is windows vs linux, then you should not worry about it, as the ways to read text almost all ignore carriage returns. load() and readmatrix() ignore carriage returns for example.
There are some commands that do not ignore carriage returns. If you fopen() a file then you can include the 't' access right, such as fopen(filename, 'rt') to make it explicit that you want carriage returns to be ignored.
