I think he won't be playing for Timor Leste once it gains official independence declaration.
As far as I know, any player can't play for other country once he plays or his name capped for one particular country. That's why player like Ryan Giggs can't play for England, because he already played for Wales before.
So, I think Miro Baldo Bento will still remain player in Indonesian NT.
I respect his decision, If Miro Baldo Bento wants to keep playing for Indonesia...sure!!!
But, your theory (Zhuge Liang) isn't correct!!! Many Croatians internationals played for Yugoslavia before Crotia became independent of yugoslavia...the same happened with Slovenia, Macedonia, Bosnia...etc...
FIFA, gives the chance to "new-born" countries to get their home born players that played for the ex-country. But that's a Miro Baldo Bento decision...
If I am not wrong, his decision to keep on playing with Indonesian NT was set when East Timor haven't had their own NT yet!
At least that's what Miro said at that time when the media asked him about his willing to play for Indonesian NT!
So, if there is East Timor NT for now, I guess he will be playing for that NT for sure!