Well, actually, the change of word order of "sedikit" in your example sentences HAS NO relationship with the word "bisa". The word "bisa" is added just to emphasize that you CAN speak a little Indonesian, but it does not affect the position of "sedikit". All of three sentences have the same meaning and are all natural. But, the problem is, the first and the third sentence are FORMAL, while the second sentence is INFORMAL so that it does not really follow the order of standard sentence. The second sentence has a slangy nuance and you can only find and use it in informal situation.

This is informal words Saya hanya bisa berbicara Bahasa Indonesia sedikit. If you want use this words Write like this : Saya hanya bisa berbicara bahasa indonesia, sedikit sih. Usually indonesian, use this words to speak informal. Form this words : S+ P + O + K S to Subjek = Saya P to Predikat = Hanya bisa berbicara O to Objek = Bahasa Indonesia K to Keterangan = Sedikit sih. Saya hanya bisa berbicara sedikit Bahasa Indonesia. << this is formal words Form This words: S + P + K + O Saya hanya berbicara sedikit Bahasa Indonesia. This is incorrect words and this is correct words : Saya bisa berbicara sedikit bahasa Indonesia. In English I can speak Bahasa not much. not much synonim with little not much = tidak banyak, sedikit. little = sedikit, kecil, tidak banyak. hope, its use Sorry my bad English.

Some words in Bahasa can change the meaning if you add it to a wrong sentence. And for that case you'd rather use the second sentence because the first sentence has different meaning but you can say it in the third sentence also. I think there's so significant rule in the kind of sentence but you just need to be careful to add up a new word because some words in Bahasa may seem the same but they will change the meaning of a sentence you make if you don't put it in a proper way.

Using informal language is not rude at all in Indonesia. In fact, we hardly talk in formal language except when it is extremely formal, like if you are a news presenter. I even use informal language when talking to my supervisors. It becomes unacceptable when you are impolite, even if you use formal language, so be careful on the words you choose instead of thinking about whether it's formal or informal. However, if you are a foreigner, we do understand that you are still learning so that even if you chose the wrong words and sound impolite, as long you do it unintentionally, it will always be fine.

But in this context, I've another question: Would it be rude, to use informal language, when talking to people as a foreigner. Or should I use formal language, when I visit that country for traveling and talk to Indonesians? I mean, I do want to be polite, but don't want to sound like a bureaucrat...