It does list the file if you open it using the Open dialog (or double click/drag to TM). But if you use the 'tm' tool it will deliberately skip it, since it's assumed that you will (in the future) open the file using that tool (again) rather than use the UI.
If you want files opened from the shell to remain on that list, use:
open -a TextMate filename
(You might want to alias that to something simpler)