I'm not going to comment on where in Indonesia they may be headed to, simply because I'm shocked that it has taken 19 seasons to get a leg in Indonesia at all. (Now I know TPTB wanted to avoid the country in the early seasons because of the possibility of terrorist attacks on westerners (such as in Bali a few years ago), but the same threat existed in the Phippines, and TAR has been there more than once.
As to why teams would take a hours-long train ride, that says to me that if nothing else production is using that time to get Phil, his crew and any other production executives traveling with the show this time ahead of the teams to film stand-ups and make sure everything is ready before the teams arrive. Production probably flew in from Jakarta, as well.
I'm just glad to see Indonesia finally get visited. Now if we could get Denmark (another country the show hasn't been to for no apparent reason) or Israel (which has been rumored more than once in the past). In one sentence, I am liking the way this season seems to be shaping up.