There is actually no bilateral recongition of pilot licences in this agreement - only a hope that in the future the agreement would be extended to include such recognition
There's no suprise; it would have been astonishing if such an agreement had been reached, for all the reasons already done to death here (e.g. the USA doesn't need it, since they hand out FAA licenses/ratings pretty easily to foreigners, etc).
On the Repair Station inspection issue, the inspection already takes place, so the EU might be objecting to the drug testing. But that is a stupid thing to object to, given the obvious safety implications of having drunken/drugged engineers in some borderline "EU country" doing maintenance work on US registered passenger jets.
So there is probably more to all this than is being said openly.