Does this happen also when started as pcmanfm-qt --daemon-mode and then instructed to open the dir with org.freedesktop.FileManager1.ShowFolders('/path/to/dir') ? If yes, I’d recommend reporting it upstream, with your reproduction scenario (slightly adjusted).
If not, maybe your shim could use this method to open the directory (after releasing the org.freedesktop.FileManager1 name, so PCManFM-Qt can take it)? Basically, your shim would just be smarter dbus activation proxy to workaround [Feature request] Support D-Bus activation for better integration with sandboxed or otherwise confined applications · Issue #2127 · lxqt/pcmanfm-qt · GitHub , not a proxy for all requests.
Yet another idea to fix the issue might be something like cd /path/to/dir && pcmanfm-qt ., but changing the working directory might have some extra side effects.