Of course it's all assumption.
As are your assumptions that they'd all get along hunky dory.
However, mine is based on an understanding of history. There's still a lot of resentment in Indian Country over broken treaties--a hundred years later. That's not an assumption. That's fact.
I agree with most of what you have said, except the last part. Again you are assuming that those resentments are still festering after another three hundred years and that isn't very realistic. However this is also an assumption based on history.
Look at it this way, the British and the Scottish have been at odds dating back to Robert the Bruce in the 13 hundreds. However when Germany threatened them in the middle twentieth century, they had a very common enemy and banded together. Heck even the Americans bonded with the English at the same time and our argument with England was less than two hundred years old.
The Scottish are BRITISH. The Welsh are BRITISH, the English are BRITISH, the people of N. Ireland are BRITISH.
And America sided with the BRITISH during WWII.
It isn't that hard, Britain (Brit, British etc..) refers to the whole of the UK, whilst English, Scottish etc. refers to one specific country within Britain.
I wasn't talking about countries, I was talking about cultures. You know in America, the south is a culture, Texans are a culture (which has latino, English, German, Native American and European influences). Native Amercian is multi cultural but are Americans too. That doesn't mean that they don't have differences and yes even issues with each other, but bottom line peoples tend to stick together when threatened from the outside. That is a human trait. So it is likely that facing the same enemy would tend to make friends of Maquis and Starfleet even in the short term.