Lithuania and Estonia didn't fight a 10 year war against the Soviets, they also didn't have their crazy religious sects gets armed and trained by a super-power and they aren't surrounded by other crazy religious nations intent on meddling. You really can't compare them
You'd be surprised.
The Forest Brothers. Some fought until the 1980s.
I asked a Lithuanian about the disparity of Russians in the Baltic States (Latvia and Estonia today are about 25% Russian speaking, while Lithuania is about 8.3% Russian speaking). My Lithuanian colleague explained, with neither shame nor pride, "We were better at killing the Russian immigrants than the other two were." And it's true. The Soviets decided to stop wasting good Russian families by moving them into remote rural Lithuanian houses, only to be murdered in their sleep. The Soviets just stopped trying.
But Bosnia and Indonesia have had their share of religious issues. I'm sure you recall Clinton engaging in Bosnia over a few of them. Indonesia, in my opinion, covers up many of the issues that they have until they make international news, like the bombing in Bali 10-15 years ago.
I sat down with a Bosnian man in a cafe in Sarajevo in 1994 and had a chat. I ordered a beer (
pivo in Serbo-Croatian) and asked him what he wanted. "
Pivo, molim." I raised my eyebrows and reminded him, "But you're a muslim." He said, "I'm a European muslim," by which he meant he is pragmatic about such things.
All that said I will agree that there are massive cultural differences. I've traveled fairly extensively in Indonesia and find their people to be largely welcoming but have never been to Afghanistan
You have the advantage over me. I've been to Afghanistan, but not Indonesia. All the Indonesians I've met, even the religious ones, struck me as pragmatic about their religion. They are sincere about their beliefs, but they are not going to club you over the head if you don't share them.