Are you sure it isn't in there? It can be hard to distinguish since it uses RLE compression to minimize the text file.
The reason i ask is that the list items are only a browsing convenience to look at one part of the table at a time.
Everything under one tab is one big table behind the scenes.
One easier way to verify if it's all there rather than looking at the text output, is to make another session, copy over the chr tiles so things are viewable, then open the produced .mt2 file in that session and see if all the contents are there.
(As an aside, VarMtClickID=64 can potentially be used as an offset if you want to extract a custom length from the full table. Be sure to click the top left metatile after switching list items but before saving the text file in order to do so reliably)
I did a test. I saved my 2x2 metatile set in a file tiles.mtt2 and added a new metatile then saved to tiles2.mtt2. I did a diff check on both files and only VarMtClickID increased. The content of the other variables remain the same even though I added one extra metatile.
Interestingly, a lot of empty lines appear at the end of bothfile. Same amount for both.
Maybe it has something to do with my second set being name Untitled? (Unable to change on Linux)