Because in Sweden, procedurally, you do not get charged until you are in custody. Largely because they don't want to make it a separate concern as you put it.
I'm my opinion this goes against european human rights. As soon as Sweden asked for him to be extradited from England, the clock starts ticking. After two years, they violated his right to a speedy trail and he is free to go.
I'm really sad that his hasn't gone to the European Court of Human Right to decide against Sweden (or England, because it is actually England that is keeping him locked up).
Note that I do not have a high opinion of Assange, and it is quite possible that according to Swedish law he did rape those women. But he should have been entitled to a trial in absentia.
No, you get convicted in absentia (assuming there is enough evidence that you did it) and then you are essentially forever a wanted criminal who still has to do some jail time.
Rather extradited – to Sweden or the US, the latter maybe via Sweden … that seems to be the real issue, not the rape accusations (although rape accusations are known as a powerful weapon to destroy enemies – although that does of course not rule out that Assange is actually a rapist under Swedish law).
I think it's quite difficult to sustain the argument that the rape accusations aren't the real issue when he's twice fled jurisdiction on the day it became certain he would be charged with rape if he didn't. If the US had wanted to try to extradite him through legal means, the US had ample opportunity to arrange it during the period Assange was calmly reporting to the UK police every day whilst his legal team tried to thwart the European Arrest Warrant on technical grounds. If they wanted to try to extradite him through illegal means they could have done so at many points during Assange's life and a high profile court case would actually be a major inconvenience.
Fleeing at convenient timing is evidence that the threat of getting arrested and extradited was real. It says nothing about the validity of the sexual assault claims.
Why can't he be charged while he's still in the Embassy?
I understand that enforcing any judgement rendered by a court becomes a hang up because of his asylum, but that's a separate concern.