This essentially requires designing a new API surface for effectively specifying these signals. The current functionality with GTKW files is not ideal but works better than nothing for specifying top-level module ports and is essentially a holdover from the past. To extend it to the VCD would require new API surface added to specify separately somehow the distinction between which traces are being dumped to the VCD and which are just being added to the GTKW.

There are various other examples that would benefit from explicitly attaching metadata of varying degrees to signals that has common meaning, one of which I view as important is eventually providing an implementation agnostic way of specifying signal attachments to a platform specific or generic implementation of an integrated logic analyzer.

This idea has been explored somewhat here: #624, but this should likely be taken up as an RFC for further development.

In the meantime I suggest a simple local patch to achieve what you want. I believe modifying the code here to check if a signal was specified in the provided traces list before adding it should be enough to workaround this issue for now.

Thank you for the pointer, I will make a local adjustment for myself in the meantime.