The single file launcher for both scummvm variants (native/libretro) can be achieved like this:

Make a folder with the ScummVM Game Id with the extension, thus sword1.svm in the roms/scummvm/ folder. Put the gamefiles into that folder, and add no *.svm in here Run scummvm from ES, select Add Game in ScummVM, select the folder sword1.svm you just created Remember / note the gameid provided by ScummVM autodetection (maybe sword1-win-gb, e.g containing some variants information)

Now, if the game id from autodetect is different than your created game id folder, there are two options to rectify the situation:

Either edit the scummvm.ini (in /opt/retropie/configs/scummvm) and change the ini section name from [sword1-win-gb] to [sword1]

Or rename the game folder from sword1.svm/ to sword1-win-gb/ in the filesystem.

You may encounter files (not directories) with the extension *.svm directly below the roms/scummvm/ folder. These are caused by the lines in +Start ScummVM.sh:

while read id desc; do echo "$desc" > "/home/pi/RetroPie/roms/scummvm/$id.svm" done < <(/opt/retropie/emulators/scummvm/bin/scummvm --list-targets | tail -n +3)

Disable/remove them to avoid having these re-appear after each ScummVM run.
Remove also the files *.svm with find $HOME/RetroPie/roms/scummvm/ -name "*.svm" -type f -exec rm -f {}

Important: Key is to have the game id folder name match the entry in the scummvm.ini for the native ScummVM the game id derived from the folder is passed to ScummVM.

In contrast lr-scummvm does not rely on *.svm files/folders at all. (Technical details: When launching lr-scummvm the absolute path of the game is passed to the libretro core. The core then searches for a *.scummvm (sic!) file with the game id in that path, if that is not found it falls back to autodetection.)

With this setup Skyscraper will detect and scrape the games properly.

Epilogue:
Also keep in mind that ScummVM and lr-scummvm are using scummvm.ini files in different locations.

ScummVM: /opt/retropie/configs/scummvm
lr-scummvm: $HOME/RetroPie/BIOS/scummvm

This setup works but may be a awkward (imposing file/foldernames, many manual steps in the right order, possibility of diversion of scummvm.ini files). Thus I came up with a more user-friendly approach, you may read the gory details in this thread

Support for ScummVM 2.6.0?