With the revelation that they are being taken, I immediately thought of Pria, from The Orville. Essentially, she was an agent from the future sent to steal The Orville for future collectors. The unidentified ship is clearly extremely powerful despite its small size, which screams time traveller to me. And they seem to be taking examples of ships from all different empires, as if for a collection.
My other thought is that it’s some party trying to turn all these empires against The Federation, as, to date, no Starfleet ships have been attacked. It’s not unreasonable that their neighbors could see that as suspicious, and conclude it’s an advanced Starfleet attack vessel.