Atlassian is an Australian company, headquartered in Sydney, though the current plc is legally in the UK. (I have no idea if that means they're bound by said backdoor law.)
They are because they provide services to Australians and have an Australian subsidiary -- just as anyone in Australia must comply with a warrant or any other lawful request by law enforcement.
If they employ a single Aussie developer, or have foreign developers on Australian soil, the government can coerce those developer to insert anything they like.
This is not quite true, though it was reported widely. The legislation doesn't consider individuals as "designated communications providers" if they work for one (unless they are self-employed or sole traders). The way it works is that your employer gets a TCN and then they disclose it to the employees necessary to implement it.
But note that if you have an Australian employee (unless they are a sole trader / contractor) you must already have an Australian subsidiary of your company (for tax and superannuation reasons).
Don't get me wrong, I am absolutely opposed to this legislation and think it is a draconian overstep of government power which (despite the PR spin doled out by the government) was absolutely not necessary for effective law enforcement. But it's best not to fall into the trap of overstating what the law actually allows the government to do.