No, I'd say that meaning was for 'aboriginal' rather than 'indigenous'.

I had to look up the etymology of 'indigenous' for this, and found an element I'd never heard of before, Latin indu- 'in'. So etymologically it just means native-born.

The Roma are indigenous to the Czech Republic, and not when they take asylum in Britain. They are not however aboriginal to either.

The aboriginal people of Italy were those there before the Romans (according to their legends that say they were founded from Troy, anyway).

Of course you can't really redefine terms on making some new archaeological discovery: say, that the Monte Verde people were aboriginal to the Americas and therefore the Clovis people weren't. It's a relative matter of time. I'd say (British) Gypsies are native (indigenous) to Britain, just as Anglo-Saxons are, but more recent arrivals like Bengalis and Czech Roma are not, even if they've been born here for a couple of generations. Give it a few more centuries. Indigenous Australians? Hm, no, 200 years isn't enough.

Same problems with animals, by the way. The rabbit is not native to Australia (200 years), but is it to Britain (1000 years)?

The dividing line could be that a native group has evolved some of its characteristics in the place where it's said to be native to. European Romany dialects differ, I believe; the dialects of English are... I think I'll stop here before I contradict myself any further.