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This is going to be a legal nightmare in near future.
Only for those accused with bone marrow transplants.
No, only for bone marrow donors. If the recipient commits a crime the donor will be the suspect.
As was said elsewhere in the comments approximate five hours before this:

> Samples of his chest and head hair, meanwhile, show only Long’s DNA.

So the donor better hope the evidence the police happens to find is hair, not sperm.
So does this mean his skin, hair, nails, etc now grow with the donor's characteristics?
Well, for the hair, no, as the article says:

> Samples of his chest and head hair, meanwhile, show only Long’s DNA.

Only because the seamen contains no sperm. The germline is unaffected by marrow transplants
Right, his red blood cells have donor DNA, and when they die they leave DNA fragments that eventually get excreted in seminal fluid.

This isn't some weird testicle transplant situation. It's closer to other stories of micro or "trace" contamination.

whose DNA will the kid have?
Semen without sperm will not produce a child, I’d imagine.
The sperm is what makes the child (along with the egg, obviously), which is what is meant by "the germline is unaffected". Thus, the child will have the DNA of the mother and the father. The donor doesn't really factor in to that story. Given the generally separate nature of testicles, it would be really surprising if that wasn't the case.