It looks like there was a solution found, so this is just for the sake of extra info:
A clipboard event typically has a number of alternative buffers stored within it, which software can use to select from, like how pasting from the text editor into Synopsis doesn’t dump a bunch of raw RTF into the field. When you copy, a TXT variant is often made. There are also “private” buffers that programs can use to communicate with themselves, using data that typically wouldn’t be understood outside of the software, which is what you’re referring to here.
Clipboard data...
A tool like the open source CopyQ can show all clipboard data, such as Scrivener’s internal extended RTF markup with styled text info.
Whether those get saved by the clipboard manager long-term is probably a function of how it is designed, but given how these special buffers are meant for private use only, they are probably only kept in memory rather than whatever persistent storage the clipboard manager uses. I’ve seen some very simple ones drop all special properties once you copy something else, meaning historic stuff is plain-text only.
P.S. The scratchpad is only a surface deep Scrivener text field. As its intended design is to be a two-way tool that writes ordinary files to the disk, it is not going to be using Scrivener-only markup like inline annotations or styles. Indeed you can set the scratchpad to write plain-text .md files and then no formatting at all will convey.