If you use detectImportOptions() with 'ExpectedNumVariables' set to the maximum column, then you can (if necessary) also use setvaropts() to set the FillValue property for each variable, which will go along with the default 'MissingRule' option value 'fill'
In practice you might be able to just
readtable(Filename, 'ExpectedNumVariables', 5)
... but beware that if you do that then the second column will probably all be interpreted as character (unless it happens to start with enough rows that are numeric... in that case, readtable() might guess that it is intended to be numeric.)
When you start getting into more complex parsing situations, and you have enough memory, then it turns out that a lot of the time it becomes easier to read the entire file as text, and then use text processing techniques, possibly involving multiple passes with regexp(), or possibly detecting boundaries and doing substring extraction and using textscan() on the resulting character vectors.
