If you know the size in advance, just stick to arrays. It is faster and perhaps easier to use (but shifting operations must be done manually with loops).

Note: a 2D array is actually an array of array objects.
Likewise, you can have an array of array lists, or an array list of arrays, and of course an array list of array lists. Etc.

Perhaps what you're searching for is a 2D masterList array to store each separate copy of 1D array fileChunks as a different row.
Take a look at this recent post to get some more details -> make-array-out-of-a-array-item

String[][] masterList;
String[]   fileChunks;

void setup() {

    String[] lookupFile = loadStrings("output.csv");
    masterList = new String[lookupFile.length][];

    for (int i = 0; i<lookupFile.length; i++) {
        fileChunks = split(lookupFile[i], ',');
        masterList[i] = fileChunks;
    }

    for ( int i = 0; i<masterList.length; println(i++ + "\n") )
        for (String master: masterList[i])    println(master);

    exit();
}

Thanks. That works and makes sense.

This is the traditional for loop -> for ( ; ; )
And this is the alternative for loop -> for ( : )

It's also nicknamed for in, foreach, and even enhanced for!

for (String master: masterList[i])    println(master);

In the traditional for loop format it would be:
for ( int master = 0; master < masterList[i]. length ; println( masterList [i] [master++] ) );

As you can see, the iterator master in the alternative for is the array + its index.
In the traditional's, the iterator is only used for the index.

Another advantage is that there's no need to know the length of an array/list when using the enhanced for loop!