Likely in the hopes that the story won't be as big a deal when she's actually released, and won't receive as much attention from potentially dangerous people.

Because the date of Manning's release (May 17th) is international LGBT day

Or, as they say in the article, that's 4 months from now, a somewhat reasonable time (considering it could have been 28 years and 4 months) to finish everything up, get her affairs on the outside settled, and all the bureaucracy done.

the commutation could have been done 2 months ago to allow for reasonable time. Also, it's not like the president doesn't have the resources or authority to accelerate it. Pardon my cynicism, but (not that I have any sympathy for the incoming president) it seems more like a political ploy to put the incoming president in a conflict where the president is tempted to do something deeply unethical to be politically consistent.

But why does she have to remain in prison until then? Can't they at least put her in the equivalent of "gardening leave"?

It's a bit of a stretch to assume the timing of this massive batch of pardons and commutes was predicated on making her release (which includes a mandatory grace period) line up with that holiday.

I would say that makes it worse. Don't you risk making it a token/pandering act instead of doing what is (arguably) the right thing to do?